Contacts of the helix formed by residues 18 - 38 (chain 0) in PDB entry 6B8H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 18 (chain 0).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150 SER 3.4 6.2 + - - -
160 THR 3.2 1.2 - - - -
170 ILE* 1.3 78.3 - - - +
190 LEU* 1.3 59.6 + - - +
200 LEU 3.2 0.9 - - - -
210 GLY* 3.3 11.9 + - - -
220 ALA 4.2 1.6 + - - -
610 THR 5.0 4.2 - - - +
620 GLY* 5.3 0.3 - - - -
650 CYS* 4.3 12.6 - - - -
161 THR 4.4 7.9 - - - -
171 ILE* 4.3 13.1 - - - +
191 LEU* 4.5 2.5 - - - -
201 LEU* 3.6 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160 THR* 3.5 14.3 + - - +
170 ILE 3.0 2.0 + - - -
180 GLY* 1.3 74.3 - - - +
200 LEU* 1.3 58.9 + - - +
210 GLY 3.1 1.8 - - - -
220 ALA* 3.2 12.6 + - + +
230 GLY* 3.0 22.3 + - - -
590 GLU* 5.2 2.9 - - - +
620 GLY* 3.6 33.4 - - - +
650 CYS* 4.0 11.9 - - - -
660 LEU* 4.8 11.4 - - + -
189 GLY 5.0 1.8 - - - -
619 THR* 3.6 35.9 - - + +
649 PHE* 3.7 24.9 - - + -
659 CYS* 3.6 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170 ILE* 3.3 34.0 + - + +
180 GLY 3.2 1.0 - - - -
190 LEU* 1.3 75.3 - - - +
210 GLY* 1.3 62.4 + - - +
230 GLY* 4.2 0.9 - - - +
240 ILE* 2.9 51.1 + - + +
201 LEU* 4.5 22.2 - - + -
241 ILE* 5.1 1.6 - - + -
179 ILE* 4.2 11.9 - - + +
189 GLY* 3.8 24.6 + - - +
209 LEU* 4.2 25.4 - - + -
219 GLY* 3.8 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180 GLY 3.3 5.9 + - - -
190 LEU 3.1 1.2 - - - -
200 LEU* 1.3 83.3 - - - +
220 ALA* 1.3 56.5 + - - +
240 ILE 3.5 0.2 + - - -
250 GLY* 2.9 23.0 + - - -
201 LEU* 3.8 20.3 - - - +
231 GLY 3.4 17.4 - - - +
241 ILE* 3.7 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180 GLY 4.2 2.0 + - - -
190 LEU* 3.2 26.2 + - + +
210 GLY* 1.3 74.5 - - - +
230 GLY* 1.3 58.2 + - - +
260 ILE* 3.0 42.7 + - + +
580 SER* 3.3 32.5 - - - +
590 GLU* 4.7 2.7 - - - +
610 THR* 4.8 0.9 + - - +
620 GLY* 4.1 10.3 - - - +
231 GLY* 4.2 3.7 - - - -
619 THR* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190 LEU 3.0 13.6 + - - -
200 LEU* 3.3 3.8 + - - -
210 GLY 3.3 0.6 - - - -
220 ALA* 1.3 78.3 - - - +
240 ILE* 1.3 60.1 + - - +
270 ALA* 3.8 6.1 + - - +
219 GLY 3.7 19.1 - - - +
229 ALA* 4.7 0.7 - - - -
259 GLY* 4.2 0.2 - - - -
589 SER* 3.7 20.5 + - - -
619 THR* 3.5 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200 LEU* 2.9 38.9 + - + +
210 GLY 4.0 2.7 - - - +
230 GLY* 1.3 75.5 - - - +
250 GLY* 1.3 59.8 + - - +
270 ALA* 3.4 5.2 + - - +
280 ILE* 2.9 46.5 + - + +
241 ILE* 4.6 19.7 - - + -
209 LEU* 5.0 1.6 - - + -
219 GLY* 3.6 22.4 - - - +
249 ILE* 4.6 23.6 - - + -
259 GLY* 4.5 3.9 - - - +
289 ILE* 4.6 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210 GLY 2.9 18.3 + - - -
220 ALA 3.1 1.3 + - - -
240 ILE* 1.3 75.9 - - - +
260 ILE* 1.3 66.1 + - - +
280 ILE* 3.0 6.5 + - - -
290 VAL* 3.0 20.5 + - - +
580 SER* 4.1 1.6 - - - -
231 GLY 3.8 5.4 - - - -
241 ILE* 4.7 2.0 - - - -
271 ALA* 3.2 30.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220 ALA 3.0 20.5 + - - +
230 GLY* 5.4 0.2 - - - -
250 GLY* 1.3 73.9 - - - +
270 ALA* 1.3 57.9 + - - +
290 VAL* 3.2 10.2 + - - +
300 PHE* 3.0 45.0 + - + -
550 PHE* 3.5 45.8 - - + +
580 SER* 3.8 17.2 + - - +
590 GLU* 3.3 31.2 - - + +
579 LEU* 4.3 6.1 - - + -
589 SER* 4.2 13.7 - - - +
619 THR* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230 GLY 3.8 2.6 + - - +
240 ILE 3.4 9.3 + - - +
250 GLY 3.1 0.6 - - - -
260 ILE* 1.3 79.2 - - - +
280 ILE* 1.3 59.2 + - - +
300 PHE* 4.4 1.8 - - - +
310 ALA* 2.8 31.4 + - - +
259 GLY* 3.2 38.8 - - - +
289 ILE* 5.0 2.0 - - + -
299 VAL* 3.4 14.9 - - + +
549 GLY 5.7 0.2 - - - -
589 SER* 3.6 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240 ILE* 2.9 40.8 + - + +
250 GLY* 3.0 9.1 + - - +
270 ALA* 1.3 74.6 - - - +
290 VAL* 1.3 58.6 + - - +
310 ALA* 3.3 5.8 + - - +
320 ALA* 3.0 28.6 + - - +
241 ILE* 4.4 18.4 - - + -
271 ALA* 4.2 9.6 - - + +
281 ILE* 4.7 12.3 - - + +
311 ALA* 3.8 20.4 - - + -
289 ILE* 4.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250 GLY 3.0 14.4 + - - +
260 ILE* 3.4 9.4 - - - +
280 ILE* 1.3 75.9 - - - +
300 PHE* 1.3 61.6 + - + +
320 ALA* 3.3 4.2 + - - +
330 LEU* 2.9 24.6 + - - +
500 MET 4.9 0.4 - - - +
510 ALA* 3.6 37.0 - - + +
540 GLY* 4.6 17.9 - - - +
550 PHE* 4.6 1.8 - - - +
580 SER* 5.6 0.2 - - - -
271 ALA* 3.7 28.5 - - + +
301 PHE* 4.5 10.5 - - + -
311 ALA* 4.7 5.6 - - - +
341 ILE* 3.8 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260 ILE* 3.0 32.6 + - + +
270 ALA* 4.1 3.6 - - - +
290 VAL* 1.3 78.0 - - + +
310 ALA* 1.3 57.1 + - - +
330 LEU* 3.3 22.1 - - + +
340 ILE* 2.9 35.2 + - + +
480 PHE* 5.2 6.3 - + - -
510 ALA* 3.9 28.9 - - + -
520 ILE* 4.4 9.0 - - + -
550 PHE* 4.0 17.7 - - + -
299 VAL* 4.3 10.8 - - + -
509 MET* 5.0 8.5 - - + +
539 LEU* 4.8 9.2 - - + -
549 GLY* 3.5 26.0 - - - -
579 LEU* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270 ALA 2.8 18.2 + - - +
280 ILE* 3.7 3.6 - - - +
290 VAL 3.2 0.2 - - - -
300 PHE* 1.3 74.4 - - - +
320 ALA* 1.3 60.2 + - - +
340 ILE* 3.2 4.1 + - - -
350 ASN* 2.9 28.5 + - - +
289 ILE* 3.6 39.9 - - + +
299 VAL* 4.1 2.2 - - - +
329 ALA* 3.3 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280 ILE 3.0 17.7 + - - +
290 VAL 3.7 2.7 - - - +
310 ALA* 1.3 74.2 - - - +
330 LEU* 1.3 60.6 + - - +
350 ASN* 3.5 4.4 + - - +
360 GLY 2.9 23.2 + - - -
311 ALA* 3.7 25.8 - - + +
341 ILE* 3.3 13.2 - - + +
351 ASN* 3.5 32.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290 VAL 2.9 13.8 + - - +
300 PHE* 3.3 23.1 - - + +
320 ALA* 1.3 76.6 - - - +
340 ILE* 1.3 56.8 + - - +
360 GLY* 3.2 1.4 + - - -
370 VAL* 3.0 45.2 + - + +
440 LYS 5.4 0.9 - - - +
470 VAL* 3.7 27.8 - - + -
480 PHE* 3.8 22.9 - - + +
510 ALA* 3.7 23.8 - - + -
341 ILE* 3.8 11.5 - - + +
509 MET* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300 PHE* 2.9 19.7 + - + +
310 ALA* 3.2 7.4 + - - +
330 LEU* 1.3 76.2 - - + +
350 ASN* 1.3 60.4 + - - +
370 VAL* 3.4 5.3 + - - +
380 SER* 3.2 23.2 + - - -
299 VAL* 3.9 36.1 - - + +
329 ALA* 3.3 28.9 - - + +
339 LEU* 3.7 3.8 - - - +
369 GLY* 5.1 3.1 - - - -
479 VAL* 3.7 30.7 - - + +
509 MET* 4.7 14.6 - - + +
519 ALA* 4.2 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310 ALA* 2.9 17.7 + - - +
320 ALA* 4.0 5.4 - - - +
340 ILE* 1.3 75.3 - - - +
360 GLY* 1.3 58.5 + - - +
380 SER* 3.9 5.4 + - - -
390 ARG* 3.5 34.3 + - - +
351 ASN* 4.4 10.3 - - - +
329 ALA* 3.4 39.3 - - - +
359 ASN* 4.2 13.8 - - - +
369 GLY* 4.4 3.1 + - - -
399 ARG* 4.8 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320 ALA 2.9 17.2 + - - -
330 LEU 3.2 2.0 + - - -
340 ILE 3.1 0.2 - - - -
350 ASN* 1.3 76.8 - - - +
370 VAL* 1.3 64.4 + - - +
380 SER 3.3 0.2 - - - -
390 ARG* 3.5 1.5 + - - -
400 ASN 3.3 20.1 + - - +
430 ILE* 4.5 2.1 - - - +
341 ILE* 4.7 2.7 - - - -
351 ASN* 4.4 4.2 + - - -
381 SER* 3.2 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330 LEU* 3.0 34.5 + - + +
340 ILE* 4.0 4.0 - - - +
360 GLY* 1.3 76.3 - - - +
380 SER* 1.3 63.1 + - - +
390 ARG 4.0 0.2 - - - -
400 ASN 3.1 24.4 - - - +
410 PRO* 3.3 15.5 - - + +
430 ILE* 5.4 1.3 - - + -
440 LYS* 4.1 42.2 - - + +
470 VAL* 6.2 0.7 - - + -
409 ASN* 5.4 0.5 + - - -
439 ILE* 4.0 24.4 - - + +
469 THR* 5.1 0.4 - - + -
479 VAL* 4.0 13.2 - - + -
509 MET* 4.8 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340 ILE 3.2 16.3 + - - -
350 ASN* 4.2 7.2 - - - -
360 GLY 3.3 0.2 - - - -
370 VAL* 1.3 77.8 - - - +
390 ARG* 1.3 59.1 + - - +
369 GLY* 3.0 39.8 + - - -
399 ARG* 3.9 21.2 - - - +
409 ASN* 3.9 18.4 + - - +
439 ILE* 4.5 14.1 - - - -
479 VAL* 5.3 1.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il