Contacts of the strand formed by residues 4 - 15 (chain H) in PDB entry 6CNC
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 4 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1H MET 4.8 4.7 + - - +
2H SER* 2.7 23.7 + - - +
3H ASN* 1.3 79.2 + - - +
5H LEU* 1.3 64.7 + - - +
7H ASP* 5.9 3.4 - - - -
58H THR* 4.3 16.8 - - + -
60H ALA* 3.7 12.3 - - + -
89H LEU* 4.1 22.9 - - + -
93H TYR* 6.4 0.9 - - + -
133H ASN* 4.3 5.4 - - - +
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Residues in contact with LEU 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H ASN* 2.9 30.5 + - - +
4H THR* 1.3 74.4 - - - +
6H PHE* 1.3 60.5 + - - +
7H ASP 4.3 1.0 + - - -
58H THR* 4.9 0.2 - - - +
59H ILE* 2.9 31.5 + - + +
60H ALA* 3.8 0.7 - - - -
61H SER* 3.7 24.5 - - - +
116H TYR* 5.1 1.1 - - - +
130H ARG 5.6 0.3 - - - +
133H ASN* 2.8 59.5 - - + +
134H ASN* 3.4 23.1 + - - +
137H GLN* 4.8 10.5 - - - +
139H ASN 6.1 0.9 - - - +
140H ALA* 6.5 0.7 - - + -
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Residues in contact with PHE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H THR 5.7 0.2 - - - -
5H LEU* 1.3 79.0 - - + +
7H ASP* 1.3 64.4 + - - +
8H ASP* 4.1 25.1 - - + -
10H PHE* 4.3 15.7 - + - -
33H GLN* 5.0 8.5 - - - -
36H CYS* 4.7 15.0 - - + -
57H VAL* 3.6 6.5 - - + +
58H THR* 3.3 5.1 - - - -
59H ILE* 3.2 40.9 + - + -
125H LEU* 4.1 35.4 - - + -
129H TYR 5.8 0.4 - - - -
130H ARG* 4.0 29.6 - - + +
134H ASN* 4.6 9.9 - - - +
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Residues in contact with ASP 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H THR* 5.9 3.8 - - - -
5H LEU 4.3 1.0 + - - -
6H PHE* 1.3 81.1 - - - +
8H ASP* 1.3 69.1 + - - +
9H ILE* 5.4 2.9 - - - +
56H THR* 3.6 15.8 - - - +
57H VAL 3.0 10.3 - - - +
58H THR* 2.5 30.3 + - + +
93H TYR* 4.0 5.9 + - - -
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Residues in contact with ASP 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H PHE* 4.1 14.6 - - + -
7H ASP* 1.3 81.4 - - - +
9H ILE* 1.3 96.1 + - - +
10H PHE* 3.6 16.0 + - + -
30H SER* 3.7 4.2 - - - -
31H THR 3.9 4.1 - - - +
32H THR* 3.8 17.0 + - - -
33H GLN* 3.5 23.0 + - - +
36H CYS* 3.5 16.3 - - - -
56H THR* 4.0 1.0 - - - -
57H VAL* 3.1 33.4 + - - +
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Residues in contact with ILE 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ASP* 5.4 3.6 - - - +
8H ASP* 1.3 94.0 + - - +
10H PHE* 1.3 74.6 + - - +
31H THR* 3.1 34.5 + - + +
32H THR* 5.3 2.0 - - - +
54H SER* 3.7 19.7 - - - +
55H LEU 3.5 7.2 - - - +
56H THR* 3.3 37.7 - - + +
145H ARG* 5.6 2.0 - - - +
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Residues in contact with PHE 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H PHE* 4.3 20.6 - + - -
8H ASP* 3.6 22.9 - - + -
9H ILE* 1.3 88.8 - - - +
11H GLN* 1.3 62.5 + - - +
28H ALA* 5.1 6.1 - - + -
29H ALA 3.2 11.4 - - - +
30H SER* 3.3 25.6 - - - +
31H THR* 4.9 1.8 - - - -
36H CYS* 4.7 4.5 - - + -
37H LYS 5.4 2.2 - - - -
38H LEU* 3.3 45.3 - - + -
54H SER* 3.5 6.1 - - - -
55H LEU* 2.8 40.0 + - + +
57H VAL* 3.5 30.1 - - + -
125H LEU* 5.3 1.8 - - + -
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Residues in contact with GLN 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H PHE* 1.3 74.9 - - - +
12H VAL* 1.3 72.7 + - - +
28H ALA* 3.2 3.6 - - - +
29H ALA* 2.9 32.8 + - + +
30H SER* 4.5 1.4 - - - +
31H THR* 4.7 8.5 - - - +
52H GLN* 3.7 35.8 - - - +
53H ASP 3.4 9.4 - - - +
54H SER* 4.8 1.1 - - - +
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLN* 1.3 82.8 - - - +
13H SER* 1.3 62.7 + - - +
14H GLU 3.9 8.5 - - - +
15H VAL* 4.1 8.5 - - + -
26H ILE* 3.6 31.6 - - + -
28H ALA* 3.6 6.1 - - + -
49H VAL* 3.9 2.0 - - + -
50H ALA 3.2 22.0 - - - +
51H ALA* 3.8 10.1 - - - -
52H GLN* 3.4 29.1 + - - +
53H ASP* 2.9 23.0 + - + +
55H LEU* 3.7 16.6 - - + -
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Residues in contact with SER 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLN 3.7 1.4 + - - -
12H VAL* 1.3 78.3 - - - +
14H GLU* 1.3 81.7 + - - +
27H GLU* 3.0 22.6 + - - -
28H ALA* 3.7 11.5 - - - +
29H ALA* 4.7 5.4 - - - -
51H ALA* 3.9 14.2 - - - +
52H GLN* 4.5 3.0 + - - +
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Residues in contact with GLU 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H VAL* 4.4 1.8 - - - -
13H SER* 1.3 109.1 + - - +
15H VAL* 1.3 71.7 + - - +
16H ASP* 4.3 15.4 - - + +
25H ARG 3.9 1.2 - - - +
26H ILE* 3.8 2.3 - - - +
27H GLU* 3.3 45.7 + - + +
51H ALA* 4.7 6.7 - - + -
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Residues in contact with VAL 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H VAL* 4.1 17.5 - - + -
14H GLU* 1.3 82.1 - - - +
16H ASP* 1.3 59.8 + - - +
17H PRO* 3.8 9.0 - - + +
24H CYS* 3.3 25.1 - - + -
25H ARG 4.1 3.4 - - - -
26H ILE* 4.3 9.6 - - + -
44H VAL* 5.5 3.6 - - + -
49H VAL* 3.9 40.6 - - + +
50H ALA* 4.3 8.7 - - - -
51H ALA* 5.1 2.3 - - - +
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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