Contacts of the strand formed by residues 91 - 99 (chain C) in PDB entry 6H7L
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 ALA 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ARG* 4.0 16.6 - - + -
39C GLN 3.5 32.3 - - - +
40C ALA* 3.5 6.5 - - + +
41C PRO* 4.9 2.9 - - - -
89C ASP 3.1 9.6 + - - +
90C THR* 1.3 77.8 - - - +
92C VAL* 1.3 62.2 + - - +
93C TYR* 3.4 7.2 - - + -
115C GLN* 3.9 9.4 - - - +
116C VAL 3.1 29.0 + - - +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.3 2.8 - - - -
39C GLN* 3.0 35.2 + - + +
91C ALA* 1.3 72.7 - - - +
93C TYR* 1.3 61.4 + - - +
94C TYR* 3.5 41.2 - - + +
112C GLN 5.0 0.9 - - - +
113C GLY* 4.2 2.9 - - - -
114C THR 3.7 21.1 - - - +
115C GLN* 3.5 21.1 - - + +
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Residues in contact with TYR 93 (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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6C GLU* 3.9 2.4 - - - +
20C LEU* 3.8 28.3 - - + -
36C TRP* 4.2 7.2 - + + -
37C TYR 3.3 7.6 - - - +
38C ARG* 3.0 37.5 + - + -
48C VAL* 3.9 18.4 - - + -
67C PHE* 3.8 6.1 - - - -
80C LEU* 4.4 4.5 - - + -
82C MET* 3.9 18.3 - - - -
89C ASP* 3.0 35.0 + - - +
91C ALA* 3.4 16.2 - - + -
92C VAL* 1.3 73.0 - - - +
94C TYR* 1.3 59.6 + - - +
113C GLY* 3.3 1.6 - - - -
114C THR* 2.9 39.9 + - + +
116C VAL* 3.5 27.2 - - + +
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Residues in contact with TYR 94 (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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6C GLU* 3.5 2.9 - - - +
36C TRP* 3.4 7.9 - - - -
37C TYR* 2.7 43.7 + - - +
38C ARG* 4.7 3.4 - - - -
39C GLN* 4.1 24.9 + - + +
45C ARG* 4.2 27.8 - - - -
92C VAL* 3.5 40.2 - - + +
93C TYR* 1.3 73.2 - - - +
95C CYS* 1.3 59.9 + - - +
96C ASN 3.9 0.3 + - - -
110C TRP* 4.0 21.1 - + + -
111C GLY 3.4 19.5 - - - +
112C GLN 3.3 19.3 - - - -
113C GLY* 3.7 9.0 - - - -
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Residues in contact with CYS 95 (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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4C LEU* 3.5 14.8 - - + +
6C GLU* 2.8 23.1 + - + +
22C CYS* 2.0 53.2 - - + -
34C MET* 5.1 0.2 - - - -
35C GLY 3.4 10.5 - - - -
36C TRP* 4.0 5.8 - - + -
78C VAL* 4.4 7.4 - - - -
94C TYR* 1.3 72.2 - - - +
96C ASN* 1.3 65.4 + - - +
97C VAL* 4.8 3.4 - - - -
110C TRP* 3.6 3.9 - - - -
111C GLY 2.8 25.8 + - - -
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Residues in contact with ASN 96 (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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33C ILE* 3.7 1.0 - - - +
34C MET* 3.4 4.9 - - - +
35C GLY* 2.9 33.5 + - - +
37C TYR* 3.4 33.0 + - + -
94C TYR 3.9 0.2 + - - -
95C CYS* 1.3 75.4 - - - +
97C VAL* 1.3 74.3 + - - +
98C LYS* 3.0 31.0 + - - +
108C ASP* 4.1 4.9 + - - -
109C TYR 2.8 26.9 + - - +
110C TRP* 3.4 30.6 - - + +
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Residues in contact with VAL 97 (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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4C LEU* 3.7 28.5 - - + -
24C ALA* 4.6 2.5 - - + -
28C ILE* 4.1 30.7 - - + -
32C ASN* 4.8 3.1 - - + -
33C ILE 3.3 6.7 - - - +
34C MET* 4.0 26.9 - - + -
95C CYS* 4.8 1.6 - - - -
96C ASN* 1.3 81.6 + - - +
98C LYS* 1.3 68.7 + - - +
99C ASP* 4.4 0.7 - - - +
107C TYR 3.7 1.7 - - - +
108C ASP* 3.5 3.8 - - - -
109C TYR* 2.9 50.1 + - + -
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Residues in contact with LYS 98 (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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32C ASN* 3.2 9.4 - - - +
33C ILE* 2.8 59.0 + - + +
37C TYR* 3.7 17.4 + - - -
96C ASN* 3.0 23.0 + - - +
97C VAL* 1.3 72.9 - - - +
99C ASP* 1.3 60.2 + - - +
100C PHE* 3.8 12.6 + - + -
106C ASP* 4.0 19.1 - - + +
107C TYR 3.7 4.5 - - - +
108C ASP* 3.3 28.4 + - - +
110C TRP* 5.0 2.2 - - - -
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Residues in contact with ASP 99 (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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284A LYS* 2.7 36.0 + - - +
287A LYS* 5.9 0.2 - - - -
28C ILE* 3.7 8.6 - - + +
29C PHE* 3.2 27.0 + - - +
32C ASN* 4.4 5.4 - - - -
97C VAL* 3.9 1.5 + - + -
98C LYS* 1.3 72.5 - - - +
100C PHE* 1.3 59.1 + - - +
101C GLY* 2.7 34.1 + - - -
102C ALA 5.0 0.2 + - - -
105C TYR 4.3 0.3 - - - +
106C ASP* 3.4 4.2 - - - -
107C TYR* 2.9 42.2 + - + +
109C TYR* 4.0 15.4 - - + -
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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