Contacts of the helix formed by residues 311 - 326 (chain A) in PDB entry 4D2W
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 ASP 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR 3.9 2.9 - - - +
74A HIS* 3.6 13.7 - - - -
75A VAL 5.0 1.1 - - - -
309A GLN* 3.2 33.3 + - + +
310A TYR* 1.3 80.8 - - - +
312A HIS* 1.3 65.5 + - - +
313A LEU* 3.4 15.6 + - - +
314A THR* 3.2 28.2 + - - -
315A ALA 3.3 7.6 + - - -
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Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.4 61.1 - + + +
30A HIS* 3.2 32.5 + + - -
32A LEU* 3.7 24.4 - - + +
74A HIS* 3.4 22.4 + - + -
293A HIS* 6.0 1.3 - + - -
311A ASP* 1.3 75.8 - - - +
313A LEU* 1.4 53.2 + - - +
315A ALA* 3.4 2.0 + - - +
316A THR* 2.7 44.0 + - - -
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 3.9 14.4 - - + -
294A HIS* 4.0 18.6 - - + +
301A MET* 3.6 24.7 - - + -
304A LEU* 3.7 48.9 - - + +
305A ILE* 3.8 19.3 - - + +
311A ASP* 3.2 16.7 + - - +
312A HIS* 1.4 75.0 - - - +
314A THR* 1.4 60.5 + - - +
316A THR* 3.3 3.9 + - - -
317A TYR* 2.9 27.9 + - - +
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Residues in contact with THR 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR 3.7 7.9 - - - +
305A ILE* 5.2 1.6 + - - +
308A TRP* 3.8 25.1 - - + -
309A GLN 3.5 8.1 + - - -
310A TYR* 2.9 48.5 + - + +
311A ASP* 3.2 7.5 + - - -
313A LEU* 1.4 77.2 - - - +
315A ALA* 1.3 57.2 + - - +
317A TYR* 3.5 4.5 + - - +
318A LEU* 3.0 51.8 + - + +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.5 24.2 - - - +
30A HIS* 4.3 8.7 - - + +
73A TYR* 3.4 28.8 + - + +
74A HIS* 4.1 3.8 - - + +
311A ASP 3.3 6.4 + - - +
312A HIS* 3.4 9.2 - - - +
313A LEU 3.3 0.6 - - - -
314A THR* 1.3 74.0 - - - +
316A THR* 1.3 61.6 + - - +
318A LEU* 3.4 1.0 + - - +
319A LEU* 2.9 39.6 + - + +
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.3 25.0 + - + -
32A LEU* 3.9 13.4 - - + +
33A THR* 4.1 1.4 - - - +
290A LEU* 3.7 22.7 - - + -
294A HIS* 6.3 0.2 - - - -
312A HIS* 2.7 34.1 + - - -
313A LEU* 3.8 5.4 - - - -
315A ALA* 1.3 75.3 - - - +
317A TYR* 1.3 56.0 + - - +
319A LEU* 4.0 0.2 - - - -
320A LEU* 2.9 32.3 + - + +
332A LEU* 3.6 28.7 - - + -
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Residues in contact with TYR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A PRO 5.9 1.1 - - - -
281A HIS 4.2 3.6 + - - -
282A LEU* 3.4 13.4 - - + +
283A ASP* 2.8 36.5 + - + +
286A CYS* 3.6 23.3 - - + -
287A VAL* 4.3 9.6 - - + -
290A LEU* 3.8 26.8 - - + +
305A ILE* 3.9 20.6 - - + -
308A TRP* 3.7 31.9 - + - -
313A LEU 2.9 18.2 + - - +
314A THR* 3.9 3.6 - - - +
316A THR* 1.3 77.1 - - - +
318A LEU* 1.3 65.9 + - + +
320A LEU* 3.4 3.6 + - - +
321A LEU* 2.9 50.9 + - + +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 4.0 31.9 - - - +
71A GLN* 3.7 28.0 - - + +
72A LEU 3.9 8.3 - - - +
73A TYR* 3.7 23.1 - - + -
308A TRP* 4.4 0.9 - - + -
314A THR* 3.0 39.4 + - + +
317A TYR* 1.3 94.4 - - + +
319A LEU* 1.3 57.9 + - - +
321A LEU* 3.5 15.3 + - + +
322A ALA* 3.1 25.6 + - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 5.3 0.7 - - + -
30A HIS* 3.4 42.2 - - + +
33A THR* 3.8 18.4 - - + +
35A GLU* 3.9 23.3 - - + +
36A MET 4.7 2.5 - - - +
37A VAL* 4.1 14.4 - - + -
73A TYR* 3.6 37.7 - - + +
315A ALA* 2.9 25.3 + - + +
318A LEU* 1.3 75.0 - - - +
320A LEU* 1.3 55.2 + - - +
322A ALA* 3.3 7.6 + - + +
323A LYS* 2.8 34.7 + - - +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 4.0 3.4 - - + +
286A CYS* 3.9 26.4 - - + +
289A GLU* 3.9 22.7 - - + -
290A LEU* 4.4 7.2 - - + -
316A THR 2.9 16.1 + - - +
317A TYR* 3.6 5.2 - - - +
319A LEU* 1.3 75.7 - - - +
321A LEU* 1.4 56.0 + - - +
323A LYS* 3.3 13.4 + - + +
324A LYS* 2.9 28.8 + - - +
330A VAL* 3.7 17.0 - - + +
331A ARG 3.6 39.0 - - - +
332A LEU* 3.9 25.1 - - + -
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASN* 6.1 3.6 - - + +
278A PRO* 5.2 14.6 - - + +
283A ASP* 3.6 37.7 - - + +
286A CYS* 3.6 8.9 - - - -
317A TYR* 2.9 38.5 + - + +
318A LEU* 3.5 17.3 - - + +
320A LEU* 1.4 73.8 - - - +
322A ALA* 1.3 57.8 + - - +
324A LYS* 3.3 7.6 + - + +
325A ALA* 3.0 26.0 + - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 5.1 6.5 - - - +
73A TYR* 5.0 6.5 - - - +
318A LEU 3.1 14.6 + - - +
319A LEU* 3.3 18.8 + - + +
321A LEU* 1.3 73.5 - - - +
323A LYS* 1.3 64.5 + - - +
325A ALA* 3.0 19.4 + - - +
326A ARG* 3.0 16.9 + - - +
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Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 3.0 33.0 + - - +
35A GLU* 3.9 17.5 + - - +
319A LEU 2.8 19.4 + - - +
320A LEU* 3.4 15.7 - - + +
322A ALA* 1.3 70.8 - - - +
324A LYS* 1.3 56.8 + - - +
326A ARG* 3.2 15.8 - - - +
328A LYS* 3.1 55.1 + - + +
329A PRO 3.4 22.0 - - - +
330A VAL* 5.8 0.2 - - - -
331A ARG* 3.1 26.8 + - - +
333A ARG 5.8 0.4 - - - +
307B LEU* 5.0 10.9 - - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASP* 3.0 37.3 + - - +
285A ASP* 3.3 25.8 - - + +
286A CYS* 4.5 2.7 - - - -
320A LEU 2.9 12.6 + - - +
321A LEU* 3.4 13.2 - - + +
322A ALA 3.1 0.2 - - - -
323A LYS* 1.3 74.4 - - - +
325A ALA* 1.4 63.3 - - - +
327A GLY* 3.2 14.2 + - - -
328A LYS 4.1 8.0 - - - +
330A VAL* 3.7 24.2 - - + +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 3.0 14.4 + - - +
322A ALA* 3.0 12.3 + - - +
324A LYS* 1.4 74.5 - - - +
326A ARG* 1.4 60.8 + - - +
327A GLY* 3.5 0.7 + - - -
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.1 38.0 + - - -
142A GLU* 2.8 37.8 + - - -
143A TYR* 3.3 32.3 + - + +
322A ALA 3.0 15.7 + - - +
323A LYS* 3.2 16.8 - - - +
325A ALA* 1.4 74.0 - - - +
327A GLY* 1.3 56.5 + - - +
328A LYS* 3.8 32.4 + - - +
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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