Contacts of the helix formed by residues 303 - 315 (chain D) in PDB entry 2W3S
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 LEU 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D PRO* 4.3 17.0 - - + +
232D GLU* 3.5 35.9 - - + +
233D SER* 4.0 9.4 - - - +
270D HIS* 4.9 0.9 - - - -
302D ASP* 1.3 95.8 + - - +
304D SER* 1.3 59.0 + - - +
305D LEU 3.4 2.7 - - - -
306D PRO* 3.1 18.1 - - + +
307D VAL* 3.0 29.4 + - + +
338D ASN 4.4 0.8 + - - -
339D THR* 4.1 0.9 - - - +
340D ALA* 3.6 27.4 - - + +
344D PHE* 4.1 9.9 - - + -
1780D XAN 4.2 13.9 - - - +
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Residues in contact with SER 304 (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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139D PHE* 5.5 2.7 - - - -
270D HIS* 2.3 42.1 + - - -
297D CYS* 3.3 27.3 + - - +
301D ALA* 3.0 20.7 + - - -
302D ASP 3.4 0.2 - - - -
303D LEU* 1.3 75.0 - - - +
305D LEU* 1.3 66.0 + - - +
307D VAL* 4.4 0.2 - - - -
308D CYS* 3.0 30.0 + - - +
330D ARG* 5.5 2.9 - - - -
338D ASN 4.0 2.8 + - - -
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Residues in contact with LEU 305 (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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140D GLU* 3.5 32.5 - - + +
301D ALA* 4.7 1.8 + - - +
302D ASP 5.3 0.4 + - - -
304D SER* 1.3 77.7 - - - +
306D PRO* 1.3 79.6 - - + +
308D CYS* 4.7 0.4 - - - -
309D ASP* 3.0 53.5 + - - +
330D ARG* 3.3 4.5 + - - +
611D ARG* 3.2 30.3 - - - +
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Residues in contact with PRO 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ASP 5.3 1.6 - - - +
303D LEU* 3.1 31.2 - - + +
305D LEU* 1.3 104.9 - - + +
307D VAL* 1.3 65.0 + - - +
309D ASP* 3.1 9.5 + - + +
310D ARG* 3.0 21.3 + - - +
344D PHE* 3.5 23.0 - - + -
460D THR* 4.7 10.0 + - - +
461D LEU* 6.3 2.7 - - + -
1780D XAN 4.2 13.7 - - - +
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Residues in contact with VAL 307 (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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269D ARG* 6.5 0.2 - - + -
270D HIS* 3.6 29.8 - - + +
272D PHE* 5.2 1.8 - - + -
303D LEU* 3.0 27.1 + - + +
304D SER 3.8 3.6 - - - +
306D PRO* 1.3 73.2 - - - +
308D CYS* 1.3 61.7 + - - +
310D ARG* 2.9 20.1 + - - +
311D ALA 3.0 11.6 + - - -
339D THR 4.0 17.0 - - - +
344D PHE* 3.3 36.3 - - + +
345D GLY* 3.3 29.4 - - - +
348D GLN* 4.9 1.3 - - - +
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Residues in contact with CYS 308 (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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270D HIS* 5.0 5.8 - - - -
272D PHE* 4.5 7.0 - - - -
293D HIS* 5.3 0.2 + - - -
295D ALA* 3.8 29.8 - - - -
297D CYS* 4.6 4.7 - - - -
304D SER 3.0 21.7 + - - +
307D VAL* 1.3 76.0 - - - +
309D ASP* 1.3 65.4 + - - +
311D ALA* 3.4 9.4 + - - +
312D MET* 3.2 24.3 + - - +
328D SER* 4.3 4.4 + - - +
330D ARG* 3.3 44.8 + - - +
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Residues in contact with ASP 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D VAL* 5.2 1.0 - - - +
146D TRP* 3.9 10.4 - - + -
305D LEU* 3.0 26.2 + - - +
306D PRO* 3.1 10.2 + - + +
308D CYS* 1.3 74.4 - - - +
310D ARG* 1.3 56.9 + - - +
312D MET* 3.2 10.0 + - - +
313D LEU* 2.8 38.9 + - + +
330D ARG* 2.4 30.1 + - - +
460D THR* 5.0 5.9 + - - +
609D TRP* 4.6 9.9 - - + -
611D ARG* 2.9 40.2 + - - +
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Residues in contact with ARG 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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306D PRO 3.0 9.0 + - - +
307D VAL 2.9 4.8 + - - +
309D ASP* 1.3 74.8 - - - +
311D ALA* 1.3 58.6 + - - +
313D LEU* 3.2 11.4 + - + +
314D HIS* 2.9 67.1 + - + +
343D GLY 3.5 13.7 - - - -
344D PHE* 3.1 33.9 - - + +
345D GLY 4.2 1.1 - - - -
346D GLY* 4.0 3.1 - - - +
455D PHE* 3.3 14.5 - - - -
456D GLY 2.7 25.7 + - - -
458D SER 2.7 31.9 + - - +
460D THR* 3.9 4.0 - - + +
529D ALA* 4.8 3.0 + - - +
619D PHE* 3.3 14.0 - - - -
730D GLU* 5.4 1.1 - - - -
1780D XAN 3.7 29.0 + - - +
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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
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272D PHE* 3.8 31.4 - - + -
293D HIS* 4.0 6.3 - - - +
307D VAL 3.0 8.6 + - - +
308D CYS 3.6 8.3 - - - +
310D ARG* 1.3 74.6 - - - +
312D MET* 1.3 63.4 + - - +
314D HIS 3.0 2.1 + - - -
315D ALA* 3.0 19.6 + - - +
345D GLY 3.2 25.1 + - - +
349D GLY* 3.3 20.3 - - - +
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Residues in contact with MET 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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144D VAL* 3.6 24.7 - - + +
146D TRP* 3.2 58.6 - - + +
293D HIS* 4.2 7.8 - - - +
308D CYS 3.2 10.8 + - - +
309D ASP* 3.3 6.3 - - - +
311D ALA* 1.3 77.5 - - - +
313D LEU* 1.3 63.9 + - - +
315D ALA* 3.1 14.6 + - - +
326D ILE* 3.6 43.1 - - + +
328D SER* 3.8 9.2 - - - -
330D ARG* 3.8 21.3 - - - -
404D HIS* 3.0 16.8 + - - -
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D TRP* 3.5 27.5 - - + -
309D ASP* 2.8 22.5 + - + +
310D ARG* 3.2 15.0 + - - +
312D MET* 1.3 73.2 - - - +
314D HIS* 1.3 66.5 + - - +
316D ASP* 3.5 3.3 - - - +
404D HIS* 3.3 9.8 - - - -
405D TYR* 3.3 42.5 + - + -
454D LYS* 5.4 0.5 + - - -
460D THR* 3.6 31.4 - - + -
609D TRP* 4.0 22.4 - - + -
618D PRO* 4.5 3.4 - - + -
619D PHE* 3.8 20.4 - - + -
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Residues in contact with HIS 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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310D ARG* 2.9 65.2 + - + +
311D ALA 3.0 2.9 + - - +
313D LEU* 1.3 77.4 - - + +
315D ALA* 1.3 56.7 + - - +
316D ASP* 3.0 10.7 - - - +
317D GLY* 2.9 23.5 + - - -
346D GLY* 3.6 23.2 - - - +
349D GLY 3.6 10.1 - - - +
350D ALA* 3.7 5.0 - - + +
405D TYR* 6.1 0.4 - - - -
454D LYS* 3.4 26.5 - - - -
455D PHE* 3.7 15.5 - + - -
456D GLY* 3.1 24.0 + - - -
619D PHE* 4.1 14.7 - + - -
622D PHE* 5.4 1.5 - + - -
734D LEU* 5.6 2.0 - - + -
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Residues in contact with ALA 315 (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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291D PHE* 3.5 17.9 - - + -
293D HIS* 4.2 10.8 - - + +
311D ALA 3.0 9.0 + - - +
312D MET 3.1 15.6 + - - +
314D HIS* 1.3 74.9 - - - +
316D ASP* 1.3 56.1 + - - +
317D GLY 3.3 0.7 - - - -
324D LEU* 4.1 3.6 - - + +
326D ILE* 3.8 24.7 - - + -
349D GLY 3.3 16.2 - - - +
353D MET* 3.1 23.6 - - - +
404D HIS* 4.5 1.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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