Contacts of the strand formed by residues 78 - 85 (chain O) in PDB entry 4C4K
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 78 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45O LYS* 4.2 4.0 - - - -
76O ASP 3.7 0.6 + - - -
77O SER* 1.3 76.6 - - - +
79O GLN* 1.3 61.9 + - - -
80O TYR* 3.9 6.9 - - - -
96O GLY* 3.4 3.1 - - - -
97O LEU* 2.8 37.9 + - - -
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Residues in contact with GLN 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O GLU 3.9 0.5 - - - +
45O LYS* 3.4 24.9 - - - +
46O ASP 4.5 2.1 + - - -
78O GLY* 1.3 71.8 - - - -
80O TYR* 1.3 64.4 + - - +
81O VAL* 3.6 13.3 - - - +
94O ALA* 3.8 20.4 - - + -
95O VAL 3.6 6.3 - - - +
96O GLY* 4.4 2.2 - - - -
9T ALA* 3.9 6.9 - - + +
10T LEU 3.0 27.1 + - - +
11T PRO* 3.5 19.3 - - - +
12T SER 4.6 1.9 + - - +
1103T EDO 3.5 14.1 + - - -
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Residues in contact with TYR 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O LEU* 3.6 24.5 - - + -
43O TRP* 4.3 8.2 - + + -
44O GLU 3.4 4.9 - - - +
45O LYS* 3.3 33.2 - - + +
50O VAL* 4.4 10.5 - - + -
56O PHE* 4.5 8.7 - + - -
67O LEU* 3.9 22.0 - - + -
69O ILE* 3.5 27.6 - - + +
76O ASP* 2.6 35.8 + - - +
78O GLY 3.9 9.0 - - - -
79O GLN* 1.3 75.0 - - - +
81O VAL* 1.3 61.3 + - - +
82O CYS 4.1 0.3 + - - -
93O ALA 4.2 0.2 - - - +
94O ALA* 3.2 2.1 - - - -
95O VAL* 2.7 43.0 + - + +
97O LEU* 3.9 18.8 - - + -
1103O EDO 5.9 0.4 - - - -
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Residues in contact with VAL 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O SER 3.9 0.2 - - - +
43O TRP* 3.3 8.0 - - - -
44O GLU* 2.8 50.4 + - + +
79O GLN* 3.6 26.2 - - + +
80O TYR* 1.3 75.0 - - - +
82O CYS* 1.3 70.5 + - - +
83O ARG* 3.9 2.5 + - + +
92O PHE* 4.1 23.8 - - + -
93O ALA 3.6 6.1 - - - +
94O ALA* 3.9 6.7 - - + +
11T PRO* 4.1 22.0 - - + -
14T ILE* 5.6 0.4 - - + -
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Residues in contact with CYS 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O PHE* 3.6 13.0 - - + -
16O PRO* 5.3 2.0 - - + -
31O CYS* 3.6 25.1 - - - -
33O ILE* 3.7 7.9 - - - -
41O VAL* 3.7 26.5 - - - -
42O SER 3.7 2.5 - - - -
43O TRP* 3.8 29.3 - - + -
80O TYR 4.1 0.4 + - - -
81O VAL* 1.3 74.3 - - - +
83O ARG* 1.3 60.6 + - - +
92O PHE* 3.3 6.8 - - - -
93O ALA* 2.7 37.2 + - + +
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Residues in contact with ARG 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O GLN* 3.7 4.4 - - - +
41O VAL* 3.3 4.0 - - - +
42O SER* 2.9 51.5 + - - +
44O GLU* 3.7 26.4 + - - +
81O VAL* 3.9 2.4 + - + +
82O CYS* 1.3 75.9 - - - +
84O ALA* 1.3 64.5 + - - +
85O ARG* 4.0 27.2 - - + +
90O GLU* 2.7 40.9 + - - +
91O ALA 3.4 4.3 - - - +
92O PHE* 3.8 29.7 - - + -
97T ARG* 4.7 13.3 - - - +
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Residues in contact with ALA 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PRO* 3.7 13.4 - - + +
12O PHE* 4.9 1.8 - - + -
33O ILE* 3.6 36.6 - - + -
39O PRO* 4.1 2.2 - - + -
40O GLN 3.4 4.7 - - - -
41O VAL* 4.0 9.6 - - + -
82O CYS 4.3 0.2 - - - -
83O ARG* 1.3 73.2 - - - +
85O ARG* 1.3 61.4 + - - +
90O GLU* 3.1 5.2 - - - +
91O ALA* 2.8 40.1 + - + +
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Residues in contact with ARG 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PRO* 4.1 0.4 - - - -
39O PRO* 3.2 5.1 - - - +
40O GLN* 2.8 89.2 + - + +
83O ARG* 4.0 31.4 - - + +
84O ALA* 1.3 75.7 - - - +
86O ASN* 1.3 65.4 + - - +
89O GLY 3.5 3.8 - - - -
90O GLU* 3.5 27.1 - - + +
20T LYS* 4.8 7.2 - - - +
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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