Contacts of the strand formed by residues 22 - 30 (chain A) in PDB entry 2D2O
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 GLN 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.2 6.8 - - - +
18A ILE* 3.0 45.9 + - + +
19A SER* 2.8 30.9 + - - +
20A GLU 3.8 0.2 - - - -
21A THR* 1.3 89.6 + - - +
23A LEU* 1.3 60.2 + - - +
24A ARG 4.1 0.2 - - - -
72A LEU* 3.7 19.0 - - + +
73A LEU 3.3 4.5 - - - +
74A GLU* 3.0 31.1 - - - +
116A ILE* 4.4 4.1 - - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 4.6 1.8 - - + -
16A TYR* 3.2 36.1 - - - +
17A PRO* 3.5 5.2 - - + -
21A THR 4.3 0.2 - - - -
22A GLN* 1.3 72.3 - - - +
24A ARG* 1.3 65.6 + - - +
25A VAL* 3.9 17.5 - - + -
72A LEU* 3.7 2.6 - - - -
73A LEU* 2.8 42.8 + - + +
75A CYS* 4.2 15.4 - - - -
80A VAL* 3.7 13.2 - - + -
82A TYR* 4.3 5.6 - - + -
113A TYR* 3.7 49.8 - - + -
116A ILE* 4.5 5.6 - - + -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR 3.9 0.7 - - - +
15A ALA* 3.3 4.9 + - - -
16A TYR* 2.8 59.3 + - + +
18A ILE* 3.9 24.1 - - + +
22A GLN 4.1 1.4 + - - -
23A LEU* 1.3 72.7 - - - +
25A VAL* 1.3 62.2 + - - +
26A ARG* 4.7 2.5 - - + -
70A GLU* 3.6 39.2 + - + +
71A ALA 3.4 8.4 + - - -
72A LEU* 4.0 27.2 - - + +
407A GLU* 2.8 40.1 + - - +
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 4.3 7.0 - - - +
14A TYR 3.2 8.7 - - - +
15A ALA* 4.4 1.3 - - + -
23A LEU* 3.9 15.9 - - + +
24A ARG* 1.3 79.7 - - - +
26A ARG* 1.3 65.1 + - - +
39A VAL* 4.2 15.9 - - + -
57A ALA* 5.5 0.2 - - - +
70A GLU* 3.3 3.8 - - - +
71A ALA* 2.9 55.8 + - + +
73A LEU* 3.7 29.2 - - + -
82A TYR* 4.3 14.6 - - + +
84A PHE* 4.4 9.4 - - + -
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 2.8 29.1 - - - -
13A SER 3.1 26.2 + - - +
14A TYR* 2.8 34.3 + - + +
16A TYR* 3.6 18.8 + - + -
24A ARG* 4.7 4.9 - - + -
25A VAL* 1.3 80.8 - - - +
27A LEU* 1.3 57.3 + - - +
68A TYR* 6.0 2.2 - - + -
69A PHE 3.1 7.2 - - - +
70A GLU* 2.8 43.3 + - + +
84A PHE* 4.9 1.3 - - - -
402A ARG* 4.6 4.4 + - - +
403A MET* 3.4 47.7 + - - +
405A TYR 2.8 29.7 + - - -
407A GLU* 4.6 6.1 - - - +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.3 5.6 - - + -
7A PHE 3.6 12.6 - - - +
8A HIS* 4.7 0.4 - - + -
14A TYR* 4.3 2.9 - - - -
26A ARG* 1.3 76.0 - - - +
28A ARG* 1.3 77.3 + - - +
29A ALA* 4.2 7.6 - - + +
37A CYS* 4.3 5.4 - - - -
68A TYR* 3.5 2.5 - - - -
69A PHE* 2.7 56.0 + - + +
84A PHE* 3.5 47.6 - - + -
86A LEU* 3.9 22.4 - - + -
96A PHE* 3.8 17.3 - - + -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA 4.5 1.5 + - - +
6A ILE* 3.2 2.9 - - - -
7A PHE* 2.9 84.5 + - + +
14A TYR* 3.3 19.0 + - - +
27A LEU* 1.3 80.2 - - - +
29A ALA* 1.3 61.2 + - - +
66A PHE* 3.5 49.1 - - + -
67A ASP 3.2 12.6 - - - +
68A TYR* 3.8 20.4 - - + -
4B GLU 5.2 2.4 + - - -
6B ILE 5.1 6.1 + - - -
7B PHE* 4.0 24.5 - - - +
28B ARG* 5.5 3.2 - - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA 3.6 8.1 - - - -
6A ILE* 3.9 14.8 - - + -
27A LEU* 4.2 7.8 - - + +
28A ARG* 1.3 75.2 - - - +
30A LYS* 1.3 70.6 + - - +
31A LYS 3.2 0.2 + - - -
33A ASP* 4.8 1.8 - - + -
34A VAL* 3.7 32.3 - - + -
66A PHE* 3.3 6.1 - - - -
67A ASP* 2.8 25.2 + - + +
69A PHE* 4.5 6.5 - - + -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.7 22.6 - - + +
5A ALA* 3.8 24.3 + - + +
6A ILE* 5.1 0.6 - - - +
29A ALA* 1.3 74.8 - - - +
31A LYS* 1.3 78.1 + - + +
32A GLY 3.2 0.7 + - - -
33A ASP* 3.0 47.2 + - - +
34A VAL 4.4 0.3 + - - -
65A ARG 3.6 10.8 - - - +
66A PHE* 4.3 2.2 - - - -
67A ASP* 4.1 1.9 - - - +
2B LEU* 5.7 3.2 - - - +
4B GLU* 3.0 30.7 + - + +
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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