Contacts of the strand formed by residues 57 - 65 (chain O) in PDB entry 3CMA
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 THR 57 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26O TRP* 5.9 1.1 - - + -
55O ASP 4.2 0.4 - - - -
56O GLU* 1.3 70.8 - - - +
58O VAL* 1.3 66.3 + - - +
59O VAL* 4.3 1.3 - - + -
75O THR* 3.5 30.5 + - + +
77O ALA* 4.0 16.4 - - + -
101O ALA* 5.4 5.2 - - + -
105O ASN* 5.1 7.7 + - - -
109O SER 5.3 0.6 + - - -
110O HIS 3.1 9.2 + - - -
111O VAL* 2.8 23.8 - - + +
112O ARG* 2.7 32.4 + - - -
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Residues in contact with VAL 58 (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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48O ILE* 4.3 14.1 - - + -
52O ALA* 3.6 31.2 - - + -
56O GLU* 4.1 7.2 - - - +
57O THR* 1.3 73.5 - - - +
59O VAL* 1.3 59.2 + - - +
60O VAL* 4.1 12.8 - - + -
74O VAL* 4.5 11.4 - - + -
75O THR 3.1 5.9 + - - -
76O VAL* 4.1 15.5 - - + -
77O ALA* 2.6 36.0 + - - +
112O ARG* 3.4 6.3 - - + +
114O ILE* 3.5 32.8 - - + -
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Residues in contact with VAL 59 (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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25O VAL* 5.8 1.3 - - + -
26O TRP* 3.6 28.7 - - + -
29O VAL* 3.7 31.4 - - + -
57O THR* 3.6 1.3 + - + -
58O VAL* 1.3 75.8 - - - +
60O VAL* 1.3 67.0 + - - +
61O PRO* 3.6 2.7 - - - +
77O ALA* 3.7 12.8 - - + -
98O LEU* 4.6 8.1 - - + -
111O VAL* 3.0 31.9 - - + -
112O ARG 2.7 11.3 + - - +
113O VAL* 3.2 13.4 - - + -
114O ILE 3.0 23.0 + - - -
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Residues in contact with VAL 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O ALA* 3.8 12.6 - - + -
43O VAL* 3.9 13.9 - - + -
48O ILE* 4.8 4.7 - - + -
58O VAL* 4.1 17.3 - - + -
59O VAL* 1.3 79.6 - - - +
61O PRO* 1.3 55.3 - - - +
62O GLY 2.6 32.9 + - - +
63O LYS 4.2 1.8 - - - +
64O VAL* 4.0 25.4 - - + -
76O VAL* 4.4 5.2 - - + -
77O ALA 3.1 11.2 + - - +
78O ALA* 3.5 17.1 + - - +
79O VAL* 3.8 2.6 + - - +
98O LEU* 4.3 3.1 - - - +
114O ILE* 3.6 22.0 - - + +
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Residues in contact with PRO 61 (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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7210 A 6.1 0.7 - - + -
29O VAL* 4.1 29.6 - - + -
32O ARG* 4.0 30.1 - - + +
33O LEU* 3.4 22.9 - - + +
40O HIS* 4.2 1.4 - - - +
41O ALA* 3.4 19.7 + - + -
59O VAL* 3.6 11.4 - - + +
60O VAL* 1.3 78.4 - - + +
62O GLY* 1.3 55.7 + - - +
79O VAL* 4.4 1.1 - - + -
113O VAL* 4.1 17.3 - - + -
114O ILE 3.7 11.9 - - - +
115O ARG* 4.9 5.8 - - + +
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Residues in contact with GLY 62 (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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33O LEU* 4.9 0.4 - - - -
40O HIS* 4.6 6.3 - - - -
41O ALA* 3.2 17.5 - - - -
60O VAL* 2.6 15.2 + - - +
61O PRO* 1.3 75.3 - - - +
63O LYS* 1.3 60.3 + - - -
78O ALA* 3.8 0.9 - - - +
79O VAL* 2.8 45.5 + - - +
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Residues in contact with LYS 63 (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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6580 C 4.1 15.1 + - + +
6590 A 2.8 76.9 + - + +
41O ALA 2.7 11.9 + - - +
42O GLU* 3.4 5.9 - - + -
43O VAL 3.0 23.4 + - - -
60O VAL* 4.2 2.5 - - - +
62O GLY* 1.3 73.7 - - - -
64O VAL* 1.3 67.4 + - - +
65O LEU* 4.1 6.1 - - + +
79O VAL* 5.7 0.2 - - + -
80O ASP* 3.0 43.3 + - + +
82O SER* 3.8 15.0 - - - +
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Residues in contact with VAL 64 (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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43O VAL* 3.3 10.5 - - + +
45O LEU* 3.9 11.7 - - + -
48O ILE* 3.8 19.3 - - + -
60O VAL* 4.0 22.0 - - + -
63O LYS* 1.3 74.5 - - - +
65O LEU* 1.3 65.8 + - - +
76O VAL* 4.1 6.1 - - + -
78O ALA* 3.5 24.9 - - - +
80O ASP 3.0 5.7 + - - -
81O PHE* 3.7 16.6 - - + -
82O SER 3.1 26.3 + - - -
85O ALA* 3.3 15.5 - - + +
89O ILE* 4.1 6.5 - - + -
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Residues in contact with LEU 65 (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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6590 A 3.6 48.7 - - + +
6600 A 3.6 10.5 - - - +
7460 A 3.3 40.8 - - + +
42O GLU* 4.5 12.3 - - + -
43O VAL 2.5 15.0 + - - +
44O ASN* 3.0 18.5 - - - +
45O LEU* 3.1 29.3 + - - +
63O LYS* 4.1 12.8 - - + +
64O VAL* 1.3 80.4 - - - +
66O GLY* 1.3 60.8 + - - +
67O SER 3.4 0.4 - - - -
82O SER* 3.9 5.4 - - - -
85O ALA* 3.6 4.0 - - - -
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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