Contacts of the strand formed by residues 68 - 73 (chain C) in PDB entry 2W93
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 68 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.2 7.4 - - - -
23C PHE* 4.9 1.1 - - - -
58C ALA* 2.8 41.9 + - - +
61C TYR* 3.8 16.8 - - - -
62C ALA* 3.6 1.3 - - - +
67C MET* 1.3 85.7 - - - +
69C CYS* 1.3 64.1 + - - +
94C GLY 3.1 3.2 + - - -
95C VAL* 3.5 16.6 - - - +
96C LEU* 2.9 26.8 + - - +
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Residues in contact with CYS 69 (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* 5.4 0.4 - - - -
14C LEU* 3.8 35.4 - - + -
19C VAL* 4.0 12.2 - - + +
21C THR 4.9 0.8 + - - -
22C VAL* 3.7 9.7 - - + -
23C PHE* 3.0 29.3 + - - -
58C ALA* 4.5 3.1 - - - -
68C SER* 1.3 79.5 - - - +
70C ILE* 1.3 64.7 + - - +
71C ILE* 4.1 12.6 - - - -
96C LEU* 3.2 16.8 - - + +
98C VAL* 3.9 23.3 - - - -
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Residues in contact with ILE 70 (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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23C PHE* 3.3 12.8 - - + +
24C GLY* 3.9 5.6 - - - -
51C GLU 3.9 5.8 - - - +
54C ALA* 3.7 9.9 - - + -
55C ALA* 3.5 35.2 - - + +
58C ALA* 4.2 9.9 - - + -
69C CYS* 1.3 74.1 - - - +
71C ILE* 1.3 65.0 + - - +
72C THR* 3.8 25.1 - - + -
81C ALA* 4.2 4.7 - - + -
85C ILE* 4.3 4.3 - - + -
95C VAL* 3.7 26.0 - - + -
96C LEU 2.9 4.9 + - - +
97C HIS* 3.4 15.4 - - + -
98C VAL* 2.8 26.5 + - - +
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Residues in contact with ILE 71 (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* 4.8 1.8 - - + -
11C PHE* 3.5 34.3 - - + -
22C VAL* 3.7 20.6 - - + -
23C PHE 2.8 11.4 + - - +
24C GLY* 3.1 23.4 - - - -
25C LEU 3.3 6.8 + - - +
30C ASN* 3.8 26.7 - - + +
33C LEU* 4.1 16.6 - - + -
34C LEU* 4.0 16.4 - - + -
45C TRP* 3.9 5.2 - - + -
69C CYS* 4.1 5.6 - - - -
70C ILE* 1.3 76.3 - - - +
72C THR* 1.3 66.8 + - - +
98C VAL* 3.2 20.4 - - + +
100C GLY 5.0 0.9 - - - +
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Residues in contact with THR 72 (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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24C GLY* 4.8 0.7 - - - -
25C LEU 4.1 4.0 - - - -
30C ASN* 3.2 13.6 + - - +
51C GLU* 3.9 13.2 - - + -
70C ILE* 3.8 21.1 - - + -
71C ILE* 1.3 80.4 - - - +
73C THR* 1.3 60.3 + - - +
77C GLY* 3.6 22.7 - - - +
78C GLU* 3.3 14.2 + - - +
81C ALA* 4.4 1.6 - - + -
97C HIS* 2.8 31.9 + - - +
98C VAL 3.0 5.1 + - - +
99C VAL* 3.5 3.9 - - - +
100C GLY 3.0 23.4 + - - -
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Residues in contact with THR 73 (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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25C LEU 4.4 1.6 + - - +
26C PRO 4.6 0.7 - - - +
27C GLY* 3.9 19.8 - - - -
29C PHE* 3.5 31.2 + - - +
30C ASN* 3.7 7.1 - - - +
51C GLU* 5.0 0.8 + - - +
72C THR* 1.3 76.1 - - - +
74C PHE* 1.3 65.9 + - - +
76C VAL* 3.7 25.6 - - + -
77C GLY* 3.0 22.8 + - - +
78C GLU* 3.1 8.8 + - - +
99C VAL* 3.9 3.4 - - - -
100C GLY 3.9 2.5 - - - -
115C HIS* 4.3 4.8 - - - +
600D TPP 4.1 20.4 - - + -
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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
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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