Contacts of the strand formed by residues 16 - 24 (chain H) in PDB entry 2ZJQ
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 16 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H VAL* 3.3 24.8 - - + +
12H ASP 4.3 5.9 - - - +
14H SER* 3.1 5.3 + - - +
15H GLY* 1.3 80.4 + - - +
17H ARG* 1.3 61.0 + - - +
19H ILE* 4.4 1.8 - - + -
55H VAL* 4.2 11.2 - - + -
58H ALA* 3.8 9.2 - - - +
64H VAL* 3.5 14.7 - - + +
98H ILE* 3.3 33.4 - - + -
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Residues in contact with ARG 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ASP* 3.8 2.8 - - - +
10H VAL* 2.9 30.9 + - - +
15H GLY 4.2 0.4 - - - +
16H ALA* 1.3 73.7 - - - +
18H GLU* 1.3 60.1 + - + +
57H ASP* 2.8 25.4 + - + +
58H ALA 4.5 3.1 - - - -
59H ALA* 3.4 38.3 - - + +
60H PRO* 4.6 7.4 - - - +
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ARG* 3.0 45.0 + - + +
8H LEU 3.3 14.5 - - - +
9H ASP* 5.2 5.6 - - - +
10H VAL* 4.0 0.2 - - - -
17H ARG* 1.3 80.0 - - + +
19H ILE* 1.3 73.5 + - - +
55H VAL* 4.1 1.2 - - - +
56H LYS* 3.4 18.4 + - + +
57H ASP* 3.1 31.0 + - + +
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Residues in contact with ILE 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ARG* 3.0 7.3 - - - -
8H LEU* 2.7 53.4 + - + +
9H ASP 5.1 0.4 - - - +
10H VAL* 3.9 17.7 - - + -
16H ALA* 4.4 4.7 - - + -
18H GLU* 1.3 82.7 - - - +
20H MET* 1.3 60.6 + - - +
21H CYS 4.0 0.3 + - - -
51H ILE* 5.1 1.3 - - + -
53H ALA* 3.9 22.7 - - + -
54H SER 3.8 8.3 - - - +
55H VAL* 4.2 20.9 - - + +
56H LYS* 4.3 1.1 - - - +
70H VAL* 5.4 1.8 - - + -
72H ALA* 3.9 23.1 - - + -
96H ALA* 4.6 12.6 - - + +
98H ILE* 4.7 10.5 - - + -
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Residues in contact with MET 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H GLN* 3.1 62.8 - - - +
7H ARG* 2.5 43.7 - - + +
8H LEU* 6.3 0.2 - - - -
19H ILE* 1.3 73.2 - - - +
21H CYS* 1.3 79.8 + - - +
53H ALA* 3.1 5.8 - - - +
54H SER* 2.9 31.9 + - - +
56H LYS* 3.7 38.9 - - + +
1684X G 5.9 0.2 - - - -
1685X A 3.8 7.0 - - - +
1935X A 6.0 3.6 - - - +
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Residues in contact with CYS 21 (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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2H ILE* 4.2 8.5 - - + -
3H MET* 3.3 38.1 - - - +
4H PRO* 3.8 3.6 - - + -
5H GLN* 3.7 8.0 + - - +
6H SER 3.1 16.5 + - - +
8H LEU* 5.9 0.2 - - - +
19H ILE 4.0 0.2 + - - -
20H MET* 1.3 91.5 - - - +
22H ILE* 1.3 71.3 + - - +
23H ARG 4.1 11.4 - - - -
24H VAL* 4.6 1.3 - - - -
51H ILE* 3.8 33.4 - - + -
52H VAL 4.1 4.5 - - - -
53H ALA* 4.3 2.9 - - - -
1935X A 5.5 1.6 + - - -
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Residues in contact with ILE 22 (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 PRO* 4.0 16.3 - - - +
21H CYS* 1.3 81.4 - - - +
23H ARG* 1.3 74.2 + - + +
52H VAL* 3.1 35.7 + - + +
53H ALA* 3.9 9.0 - - - +
54H SER* 3.9 17.9 - - - -
69H VAL* 4.6 5.4 - - + -
1935X A 3.3 69.5 + - + +
2527X G 5.1 4.7 + - - +
2539X C 4.6 1.8 - - - +
2540X A 4.3 12.8 - - - +
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Residues in contact with ARG 23 (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 PRO* 4.6 7.6 - - + -
21H CYS* 4.1 0.9 - - - -
22H ILE* 1.3 87.2 - - + +
24H VAL* 1.3 68.8 + - - +
25H LEU* 3.2 40.4 + - - +
40H GLY 5.3 4.6 + - - -
41H ASN 5.9 0.4 + - - -
51H ILE* 3.5 3.2 - - - -
52H VAL* 3.0 25.5 + - - +
2526X U 4.7 5.6 + - - -
2527X G 5.2 6.7 - - - +
2540X A 2.3 66.0 + - + +
2541X U 2.3 54.2 + - - -
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Residues in contact with VAL 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H ILE 3.9 20.0 - - - +
3H MET* 4.3 1.8 - - - -
4H PRO* 4.3 15.2 - - + +
21H CYS* 4.6 2.2 - - - -
23H ARG* 1.3 82.6 + - - +
25H LEU* 1.3 71.1 + - - +
26H ASN 3.7 0.9 + - - -
41H ASN 4.2 13.0 - - - +
42H LYS* 3.7 42.1 - - + +
43H ARG 4.0 11.7 - - - +
44H TYR 4.0 6.7 - - - +
45H ALA* 4.0 15.0 - - + +
49H ASP* 5.4 0.4 - - + -
50H ILE 4.6 1.8 - - - +
51H ILE* 4.2 8.5 - - + -
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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