Contacts of the strand formed by residues 205 - 213 (chain C) in PDB entry 2WFK
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 205 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C TYR* 3.6 13.6 - - - -
44C VAL* 2.9 31.6 + - - +
105C GLU 4.7 0.2 - - - -
110C HIS* 4.3 16.2 - - - -
111C TRP* 4.3 1.3 - - - -
112C PHE* 3.6 13.5 - - - -
204C LYS* 1.3 78.7 - - - +
206C SER* 1.3 65.0 + - - -
207C PHE* 4.6 0.2 - - - -
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Residues in contact with SER 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLY 3.5 11.7 - - - -
43C TYR* 3.6 15.1 - - - -
80C SER* 2.6 29.7 + - - -
81C PRO* 3.5 4.9 - - - +
82C THR* 2.9 42.1 + - - -
98C PHE* 4.2 2.9 - - - -
105C GLU 4.6 2.0 + - - -
106C LYS* 3.2 24.7 + - - -
110C HIS 4.6 2.6 + - - -
112C PHE* 4.0 0.3 - - - -
205C GLY* 1.3 72.7 - - - -
207C PHE* 1.3 60.9 + - - +
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Residues in contact with PHE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TYR* 4.2 29.4 - + - -
41C TYR* 3.6 2.9 - - - +
42C GLY* 2.9 60.8 + - - +
43C TYR 3.9 2.7 - - - -
44C VAL* 4.1 17.3 - - + -
61C TYR* 4.3 22.7 - + + -
78C MSE 3.5 38.8 - - + -
79C ILE 3.1 14.1 - - - +
80C SER* 4.2 2.2 - - - -
82C THR* 3.3 10.8 - - - +
112C PHE* 3.9 15.0 - + + -
195C PHE* 4.3 4.3 - - + -
205C GLY 4.6 0.2 - - - -
206C SER* 1.3 78.3 - - - +
208C VAL* 1.3 60.5 - - - +
209C ALA* 4.1 14.4 - - + -
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.1 23.1 - - + -
39C ASN* 4.5 1.6 - - + -
40C TYR 3.4 4.9 - - - +
41C TYR* 3.6 37.0 - - + +
77C ARG* 4.0 1.8 - - - +
78C MSE 3.5 1.6 - - - -
79C ILE* 2.9 56.4 + - + +
82C THR* 3.8 18.8 - - + -
85C ILE* 5.1 7.2 - - + -
207C PHE* 1.3 76.5 - - - +
209C ALA* 1.3 70.2 + - - +
210C SER* 4.2 1.6 + - - +
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE 3.7 0.3 - - - +
39C ASN* 3.2 5.2 - - - +
40C TYR* 2.7 48.4 + - + +
63C LEU* 5.1 0.7 - - + -
77C ARG 3.3 4.5 - - - -
78C MSE 4.4 0.9 - - - +
195C PHE* 3.3 46.0 - - + -
207C PHE* 4.1 8.9 - - + -
208C VAL* 1.3 74.4 - - - +
210C SER* 1.3 62.9 + - - +
211C VAL* 5.4 0.4 - - - -
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.9 4.0 - - - +
10C LEU* 4.0 19.0 - - - +
37C VAL* 4.9 1.1 - - - -
38C ILE 3.3 4.5 - - - -
39C ASN* 2.7 23.9 + - - -
76C VAL* 3.4 5.5 - - - +
77C ARG* 2.9 64.7 + - - +
208C VAL* 4.6 1.2 - - - +
209C ALA* 1.3 74.5 - - - +
211C VAL* 1.3 66.9 - - - +
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.2 3.4 - - - -
36C SER 3.8 0.7 - - - +
37C VAL* 3.2 4.8 - - - +
38C ILE* 2.9 42.5 + - + +
63C LEU* 3.8 25.4 - - + -
65C VAL* 4.7 2.9 - - + -
74C MSE 4.6 7.0 - - + -
75C GLY 3.3 7.6 - - - +
76C VAL* 4.8 0.9 - - + -
193C ILE* 3.7 33.4 - - + -
195C PHE* 4.0 8.1 - - + -
210C SER* 1.3 80.9 - - - +
212C GLY* 1.3 66.3 + - - +
213C LEU* 4.6 2.9 - - + -
226C ILE* 3.8 22.1 - - + +
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Residues in contact with GLY 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.9 2.5 - - - +
34C TYR* 3.6 26.5 - - - -
36C SER 3.3 7.6 - - - -
37C VAL* 4.2 3.1 - - - -
74C MSE 3.3 6.4 - - - +
75C GLY 2.8 33.5 + - - +
211C VAL* 1.3 74.5 - - - +
213C LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 3.5 5.2 - - - -
35C GLY 3.0 16.5 + - - -
36C SER* 3.1 22.6 + - - +
65C VAL* 3.9 9.4 - - + -
67C ILE* 4.7 0.4 - - + -
71C ILE* 4.6 14.6 - - + -
73C GLU 3.8 2.7 - - - +
74C MSE 3.5 47.3 - - + -
211C VAL* 4.6 2.0 - - + -
212C GLY* 1.3 74.1 - - - -
214C LEU* 1.3 60.3 + - - +
215C PHE 2.9 9.4 + - - +
224C PRO* 3.4 37.7 - - + -
226C ILE* 3.6 30.7 - - + -
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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