Contacts of the helix formed by residues 278 - 288 (chain A) in PDB entry 2WSK
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.8 3.3 - - - +
93A ILE* 3.5 25.6 - - - +
95A PRO* 4.7 6.7 - - - +
224A VAL 4.6 8.6 + - - -
267A SER* 5.9 1.0 - - - -
269A GLU* 2.8 14.5 + - - +
276A LEU* 4.2 0.4 - - - +
277A PHE* 1.3 79.8 - - - +
279A LEU* 1.3 91.8 + - - +
280A ARG 3.2 1.8 - - - -
281A GLY* 2.8 16.5 + - - -
282A ILE* 3.0 23.0 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.8 25.4 - - + -
226A MET* 5.2 5.6 - - + -
267A SER* 4.1 14.6 - - - -
269A GLU* 3.3 7.3 + - - +
278A SER* 1.3 89.9 + - - +
280A ARG* 1.3 64.3 + - - +
282A ILE* 4.4 3.1 - - + -
283A ASP 3.0 23.4 + - - -
284A ASN 3.3 6.2 + - - -
287A TYR* 3.6 39.2 - - + -
288A TYR* 3.3 31.0 - - + +
306A LEU* 4.3 17.7 - - + -
316A TYR* 4.9 7.0 - - + +
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Residues in contact with ARG 280 (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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85A ARG* 3.7 30.8 - - + +
86A PHE* 5.6 0.5 - - - -
112A ALA* 4.4 11.4 - - + +
269A GLU* 2.8 43.1 + - - +
270A LEU 2.8 28.7 + - - -
271A ASP 2.9 14.2 + - - -
272A LEU* 4.6 9.3 + - - +
274A GLY 3.3 13.9 + - - -
275A PRO 3.1 27.3 + - - -
276A LEU* 3.8 15.9 - - + +
278A SER 3.0 0.6 + - - -
279A LEU* 1.3 74.3 - - - +
281A GLY* 1.3 61.1 + - - +
284A ASN* 3.3 32.5 + - - +
288A TYR* 4.0 0.8 + - - -
296A TYR* 2.6 29.6 + - - +
304A ASN* 4.5 0.8 - - - +
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Residues in contact with GLY 281 (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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74A VAL* 3.4 7.6 - - - +
85A ARG 4.0 12.6 - - - -
86A PHE* 3.4 23.8 - - - -
87A ASN 4.9 2.5 + - - -
92A LEU* 3.2 25.5 - - - +
276A LEU* 3.4 13.4 - - - +
278A SER 2.8 4.8 + - - -
280A ARG* 1.3 78.0 - - - +
282A ILE* 1.3 59.3 + - - +
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Residues in contact with ILE 282 (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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25A LEU* 4.4 17.7 - - + -
26A PHE 3.2 26.9 - - - +
27A SER* 2.6 31.0 + - - -
72A TYR* 5.8 1.6 - - + -
74A VAL* 4.1 11.0 - - + +
86A PHE* 2.9 12.3 - - - -
92A LEU* 3.6 14.4 - - + -
93A ILE 3.7 9.4 - - - +
95A PRO* 3.5 34.8 - - + -
278A SER* 3.0 26.6 + - - +
279A LEU* 3.2 6.9 + - + +
281A GLY* 1.3 79.6 - - - +
283A ASP* 1.3 56.0 + - + +
287A TYR* 4.3 9.9 - - + +
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Residues in contact with ASP 283 (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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26A PHE* 3.9 1.2 - - + -
27A SER* 3.8 8.4 - - - +
28A ALA 2.7 27.3 + - - -
29A HIS* 3.0 30.0 + - - +
86A PHE* 4.0 6.8 - - - -
279A LEU 3.0 7.9 + - - -
281A GLY 3.7 0.4 - - - -
282A ILE* 1.3 82.3 - - - +
284A ASN* 1.3 63.6 + - - +
285A ARG* 3.5 3.3 + - - +
286A SER* 2.6 34.5 + - - -
287A TYR* 3.0 33.5 + - + -
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Residues in contact with ASN 284 (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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83A GLY* 3.0 26.9 + - - +
84A HIS* 5.8 0.4 - - - +
85A ARG* 3.9 22.4 - - - +
86A PHE* 5.1 2.0 - - - -
272A LEU* 5.5 1.0 - - - +
279A LEU 3.3 8.2 + - - -
280A ARG* 3.3 21.5 + - - +
283A ASP* 1.3 73.3 + - - +
285A ARG* 1.3 61.8 + - - +
288A TYR* 3.2 36.3 + - - +
290A ILE* 3.3 19.0 - - - +
294A GLY 4.8 3.6 + - - -
296A TYR* 2.7 38.2 + - - -
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Residues in contact with ARG 285 (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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29A HIS* 3.8 17.1 + - + -
82A GLU* 3.4 40.5 + - - +
83A GLY* 3.6 5.9 + - - +
84A HIS* 3.7 36.6 + - + +
283A ASP* 3.2 6.0 + - - +
284A ASN* 1.3 78.5 - - - +
286A SER* 1.3 59.9 + - - +
288A TYR 3.5 11.8 - - - +
290A ILE* 4.2 21.6 - - + +
291A ARG 5.8 0.8 + - - -
307A ASN* 5.8 0.7 + - - -
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.9 18.4 - - - -
28A ALA* 3.6 7.4 - - - +
29A HIS* 3.3 15.1 + - - -
283A ASP* 2.6 33.9 + - - -
285A ARG* 1.3 79.6 - - - +
287A TYR* 1.3 65.1 + - - +
288A TYR 3.5 0.7 + - - -
307A ASN* 3.9 12.3 + - - +
310A HIS* 3.9 25.4 + - - -
313A VAL* 3.8 11.7 - - - +
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Residues in contact with TYR 287 (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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25A LEU* 5.7 0.2 - - - +
26A PHE* 3.7 36.8 + + - +
95A PRO* 4.0 16.7 - - + +
279A LEU* 3.6 56.8 - - + -
282A ILE* 4.3 18.8 - - + -
283A ASP* 3.0 26.1 + - + +
286A SER* 1.3 78.0 - - - +
288A TYR* 1.3 60.1 + - + +
306A LEU* 3.3 13.4 - - + +
307A ASN* 2.7 27.6 + - - -
312A ALA 5.6 0.2 - - - -
313A VAL* 4.0 25.0 - - + +
316A TYR* 4.4 31.2 - + + +
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Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A SER* 2.5 28.2 + - - -
269A GLU* 2.8 18.6 + - + -
279A LEU* 3.3 27.2 - - + +
280A ARG 4.0 2.0 - - - -
284A ASN* 3.2 32.6 + - - -
285A ARG 3.5 11.3 - - - +
286A SER 4.1 1.9 - - - +
287A TYR* 1.3 80.1 - - + +
289A TRP* 1.3 60.9 + - - +
290A ILE* 2.9 27.8 + - + +
296A TYR* 3.6 18.8 - + + -
304A ASN* 3.2 39.5 + - + -
305A THR 3.5 13.7 - - - +
306A LEU* 3.6 17.7 - - + -
307A ASN* 4.1 7.8 + - - +
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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