Contacts of the helix formed by residues 307 - 326 (chain D) in PDB entry 4RZR
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 SER 307 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D TYR* 3.2 3.1 + - - -
305D GLY 3.9 3.4 + - - -
306D ILE* 1.3 80.1 - - - +
308D LYS* 1.3 59.7 + - - +
309D GLU* 3.4 18.6 - - - +
310D THR* 2.7 33.9 + - - -
311D ALA 2.9 22.7 + - - -
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Residues in contact with LYS 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ILE* 4.5 0.2 - - + -
270D GLU* 3.3 40.1 + - - +
273D TYR* 3.8 50.0 + - + +
307D SER* 1.3 72.4 - - - +
309D GLU* 1.3 64.5 + - - +
311D ALA* 3.0 5.5 + - - +
312D TYR* 2.9 46.3 + - + -
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Residues in contact with GLU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D SER* 3.4 22.0 - - - +
308D LYS* 1.3 81.3 + - - +
310D THR* 1.3 62.8 + - - +
312D TYR* 3.3 9.8 + - - +
313D SER* 2.9 29.5 + - - -
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Residues in contact with THR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D PHE* 4.2 26.7 - - + -
304D HIS* 5.8 2.9 - - - +
305D GLY 5.8 0.4 - - - +
306D ILE* 4.1 13.2 - - + -
307D SER* 2.7 29.7 + - - -
309D GLU* 1.3 79.4 - - - +
311D ALA* 1.3 53.9 + - - +
313D SER* 4.4 5.2 - - - -
314D GLU* 2.7 36.0 + - + +
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Residues in contact with ALA 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ILE* 4.1 7.4 - - + -
273D TYR* 3.7 24.7 - - + -
284D ILE* 3.8 7.1 - - - +
306D ILE* 3.6 12.9 - - + +
307D SER 2.9 14.8 + - - +
308D LYS 3.2 9.0 - - - +
310D THR* 1.3 72.8 - - - +
312D TYR* 1.3 66.9 + - - +
314D GLU* 4.7 0.2 - - - -
315D SER* 2.9 27.1 + - - -
337D PHE* 3.9 15.0 - - + -
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Residues in contact with TYR 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D PHE* 3.6 55.5 + + + +
269D ILE* 3.4 25.4 - - + -
270D GLU* 2.4 43.2 + - - +
308D LYS* 2.9 37.3 + - + -
309D GLU* 3.5 10.8 - - - +
311D ALA* 1.3 71.3 - - - +
313D SER* 1.3 63.1 + - - +
315D SER* 2.6 24.8 + - - -
316D VAL* 3.3 12.5 + - - +
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Residues in contact with SER 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D GLU 2.9 17.3 + - - -
310D THR* 3.8 6.9 - - - +
312D TYR* 1.3 76.4 - - - +
314D GLU* 1.3 62.4 + - - +
316D VAL* 3.4 14.9 + - - +
317D LYS* 3.5 28.8 + - - +
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Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D ILE* 4.1 17.5 - - + -
300D ARG* 3.3 40.3 + - - +
302D PHE* 3.8 25.6 - - + -
306D ILE* 5.9 0.2 - - + -
310D THR* 2.7 25.9 + - + +
311D ALA* 4.2 2.7 - - - +
313D SER* 1.3 72.8 + - - +
315D SER* 1.3 65.6 + - - +
317D LYS* 3.3 28.9 + - - +
318D LEU* 3.0 34.5 + - + +
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Residues in contact with SER 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D LEU* 3.7 15.0 - - - +
266D PHE* 4.0 3.1 - - - -
269D ILE* 3.2 26.2 - - - +
284D ILE* 4.2 8.9 - - - +
286D VAL* 3.5 26.5 - - - +
311D ALA 2.9 14.1 + - - -
312D TYR* 2.6 19.6 + - - -
314D GLU* 1.3 76.0 - - - +
316D VAL* 1.3 56.6 + - - +
318D LEU* 3.3 0.9 + - - -
319D LEU* 2.9 28.6 + - - +
335D VAL* 5.3 0.4 - - - -
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Residues in contact with VAL 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D LEU* 4.6 7.0 - - + -
262D LYS* 4.1 28.0 - - + -
265D LEU* 4.6 2.7 - - + -
266D PHE* 3.6 29.8 - - + -
312D TYR 3.3 14.0 + - - +
313D SER* 3.8 9.0 - - - +
314D GLU 3.2 0.8 - - - -
315D SER* 1.3 77.8 + - - +
317D LYS* 1.3 57.9 + - + +
319D LEU* 3.0 9.0 + - - +
320D GLN* 2.8 47.0 + - + +
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Residues in contact with LYS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ARG* 5.4 3.6 - - - +
313D SER* 3.5 23.0 + - - +
314D GLU* 3.3 34.3 + - - +
316D VAL* 1.3 78.6 - - + +
318D LEU* 1.3 58.9 + - + +
320D GLN* 3.4 17.7 + - - +
321D LYS* 2.9 26.9 + - - +
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D ILE* 4.1 24.7 - - + +
286D VAL* 3.6 25.6 - - + +
298D ARG* 3.6 34.2 - - + +
299D GLY* 3.9 25.8 - - - +
300D ARG* 4.4 1.8 - - + +
314D GLU* 3.0 34.4 + - + +
315D SER 3.7 0.7 - - - +
316D VAL 3.1 0.2 - - - -
317D LYS* 1.3 74.6 - - + +
319D LEU* 1.3 66.6 + - - +
321D LYS* 3.3 15.7 + - + +
322D ILE* 3.0 27.1 + - - +
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D LEU* 3.6 28.3 - - + +
261D ILE* 3.6 28.0 - - + -
262D LYS* 4.7 5.2 - - + +
265D LEU* 3.9 20.6 - - + -
286D VAL* 4.5 6.6 - - + +
315D SER 2.9 13.4 + - - +
316D VAL* 3.3 9.2 - - - +
318D LEU* 1.3 76.8 - - - +
320D GLN* 1.3 56.5 + - - +
322D ILE* 3.1 10.4 + - + +
323D LEU* 3.0 32.5 + - + +
330D ILE* 4.1 20.6 - - + -
333D ILE* 3.8 24.0 - - + -
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Residues in contact with GLN 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D LEU* 3.6 35.0 - - + +
316D VAL* 2.8 20.1 + - - +
317D LYS* 3.5 29.4 + - - +
319D LEU* 1.3 78.6 - - - +
321D LYS* 1.3 61.0 + - - +
323D LEU* 3.4 8.9 + - + +
324D GLU* 3.1 37.4 + - + +
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Residues in contact with LYS 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D ARG* 3.8 31.0 - - + +
317D LYS 2.9 14.2 + - - +
318D LEU* 3.4 19.1 - - + +
319D LEU 3.3 0.2 - - - -
320D GLN* 1.3 74.9 - - - +
322D ILE* 1.3 62.8 + - - +
324D GLU* 3.5 10.7 + - - +
325D GLU* 3.0 63.3 + - - +
7F A 4.2 8.3 - - - -
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Residues in contact with ILE 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D VAL* 3.8 35.0 - - + +
288D ALA* 4.0 31.4 - - + -
290D THR* 6.4 1.1 - - + -
296D VAL* 4.2 23.8 - - + +
298D ARG* 3.5 24.5 - - + +
318D LEU 3.0 18.0 + - - +
319D LEU* 3.1 10.7 + - + +
321D LYS* 1.3 76.2 - - - +
323D LEU* 1.3 57.8 + - - +
325D GLU* 3.2 2.5 + - - -
326D ASP* 2.9 36.2 + - + +
330D ILE* 4.2 14.8 - - + -
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Residues in contact with LEU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D ARG* 3.2 64.2 + - + +
258D LEU* 4.1 29.4 - - + -
261D ILE* 4.3 6.3 - - + -
319D LEU* 3.0 26.8 + - + +
320D GLN* 3.9 6.3 - - + +
322D ILE* 1.3 75.3 - - - +
324D GLU* 1.3 60.0 + - + +
326D ASP 3.0 18.6 - - - +
327D GLU* 5.0 0.3 - - - -
328D ARG 5.2 0.2 - - - +
330D ILE* 3.6 29.4 - - + -
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Residues in contact with GLU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D GLN* 3.1 29.7 + - + +
321D LYS* 3.9 12.6 - - - +
322D ILE 3.3 0.2 - - - -
323D LEU* 1.3 77.0 - - + +
325D GLU* 1.3 66.9 + - + +
326D ASP 3.7 0.7 + - - -
327D GLU* 6.0 1.4 - - - +
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Residues in contact with GLU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D ARG* 2.6 43.8 + - - +
321D LYS* 3.0 52.1 + - + +
322D ILE 4.2 1.1 - - - +
324D GLU* 1.3 86.3 - - + +
326D ASP* 1.3 60.8 + - - +
327D GLU* 5.8 1.9 - - - +
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Residues in contact with ASP 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ARG* 2.3 27.7 + - - -
290D THR* 4.4 6.9 - - - +
296D VAL* 3.9 16.9 - - + +
298D ARG* 6.0 0.9 - - - +
322D ILE* 2.9 22.7 + - + +
323D LEU* 3.0 6.9 - - - +
324D GLU 3.4 0.8 - - - -
325D GLU* 1.3 80.3 - - - +
327D GLU* 1.3 54.4 + - - +
328D ARG* 2.7 59.6 + - - +
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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) + - + + + + + -
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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