Contacts of the helix formed by residues 2 - 19 (chain A) in PDB entry 2GRR
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 SER 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 77.4 + - - +
3A GLY* 1.3 58.4 + - - +
4A ILE 3.2 3.6 - - - -
5A ALA* 3.0 4.1 + - - +
6A LEU* 2.9 43.2 + - - +
39A MET* 4.2 12.5 - - - +
66A ASP* 3.7 39.3 - - - -
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Residues in contact with GLY 3 (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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1A MET* 3.4 4.6 - - - +
2A SER* 1.3 77.3 + - - +
4A ILE* 1.3 56.8 + - - +
6A LEU* 3.8 11.2 - - - +
7A SER* 3.0 32.6 + - - -
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Residues in contact with ILE 4 (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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1A MET 5.2 1.5 + - - +
2A SER 3.2 1.0 - - - -
3A GLY* 1.3 73.1 - - - +
5A ALA* 1.3 67.3 + - - +
7A SER* 3.2 7.9 + - - -
8A ARG* 3.2 22.0 + - + +
66A ASP 5.9 0.7 - - - +
68A TYR 4.5 8.5 - - - +
69A PRO* 4.6 9.6 - - + -
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Residues in contact with ALA 5 (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 SER 3.0 9.0 + - - +
4A ILE* 1.3 79.1 - - - +
6A LEU* 1.3 56.7 + - - +
8A ARG* 3.3 3.8 + - - +
9A LEU* 2.9 34.9 + - - +
39A MET* 4.0 19.1 - - + -
66A ASP 3.9 14.4 + - - +
68A TYR* 3.3 42.1 + - + +
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Residues in contact with LEU 6 (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 SER* 2.9 35.6 + - - +
3A GLY* 3.8 8.5 - - - +
5A ALA* 1.3 74.2 - - - +
7A SER* 1.3 65.0 + - - +
9A LEU* 4.4 2.2 - - - -
10A ALA* 3.0 25.8 + - - +
38A LEU* 3.8 30.9 - - + +
39A MET* 3.7 28.5 - - + -
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Residues in contact with SER 7 (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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3A GLY 3.0 18.7 + - - -
4A ILE* 3.2 8.6 + - - -
6A LEU* 1.3 77.1 - - - +
8A ARG* 1.3 65.0 + - - +
10A ALA* 3.5 5.8 + - - +
11A GLN* 3.4 23.4 + - - +
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Residues in contact with ARG 8 (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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4A ILE* 3.2 10.1 + - + +
5A ALA* 3.8 6.1 - - - +
7A SER* 1.3 80.4 - - - +
9A LEU* 1.3 57.3 + - - +
11A GLN* 3.0 10.0 + - + +
12A GLU* 2.8 47.4 + - + +
68A TYR* 3.0 36.8 + - + -
69A PRO* 3.8 30.7 - - + +
103A TRP* 4.2 6.1 - - - -
105A PRO* 2.9 28.1 + - - +
107A ILE 2.8 29.3 + - - -
108A THR* 4.7 1.0 - - - +
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Residues in contact with LEU 9 (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* 2.9 23.9 + - + +
6A LEU 4.0 1.8 - - - +
8A ARG* 1.3 75.5 - - - +
10A ALA* 1.3 57.7 + - - +
12A GLU* 3.6 20.6 - - - +
13A ARG* 2.9 30.1 + - - +
38A LEU* 3.3 37.4 - - + +
39A MET* 3.7 23.8 - - - -
41A TRP* 3.9 13.2 - - + +
64A PHE* 3.7 36.6 - - + -
68A TYR* 3.6 18.2 - - + -
109A ILE* 4.9 0.2 - - + -
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Residues in contact with ALA 10 (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 LEU 3.0 18.3 + - - +
7A SER* 3.7 6.7 - - - +
8A ARG 3.2 0.2 - - - -
9A LEU* 1.3 76.3 - - - +
11A GLN* 1.3 71.5 + - - +
13A ARG* 3.4 6.1 + - - +
14A LYS* 3.2 28.3 + - + +
36A MET* 6.1 1.6 - - + -
38A LEU* 3.9 18.1 - - + +
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Residues in contact with GLN 11 (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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7A SER 3.4 13.4 + - - +
8A ARG* 3.0 10.8 + - + +
10A ALA* 1.3 81.9 - - - +
12A GLU* 1.3 59.5 + - + +
14A LYS* 3.3 30.4 + - - +
15A ALA* 2.9 29.7 + - - +
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Residues in contact with GLU 12 (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 ARG* 2.8 46.8 + - + +
9A LEU* 3.2 13.7 + - - +
11A GLN* 1.3 77.0 - - + +
13A ARG* 1.3 57.2 + - - +
15A ALA* 3.7 5.8 - - - +
16A TRP* 2.9 31.4 + - - +
41A TRP* 4.1 2.0 - - + -
68A TYR* 2.5 37.4 + - - -
108A THR* 4.3 5.0 - - - +
109A ILE* 3.9 37.7 + - + +
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Residues in contact with ARG 13 (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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9A LEU 2.9 16.8 + - - +
10A ALA* 3.6 6.3 + - - +
11A GLN 3.2 0.2 - - - -
12A GLU* 1.3 77.0 - - - +
14A LYS* 1.3 72.3 + - - +
16A TRP* 3.3 2.9 + - - +
17A ARG* 2.9 79.1 + - + +
28A PRO* 4.0 17.8 - - + +
36A MET* 3.2 42.7 - - - +
38A LEU* 4.3 2.7 - - + -
41A TRP* 3.6 19.2 - - + -
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Residues in contact with LYS 14 (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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10A ALA* 3.2 13.9 + - + +
11A GLN* 3.3 34.5 + - - +
13A ARG* 1.3 91.9 - - - +
15A ALA* 1.3 56.4 + - - +
17A ARG* 3.4 8.7 + - - +
18A LYS* 3.0 28.8 + - - +
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Residues in contact with ALA 15 (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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11A GLN 2.9 17.6 + - - +
12A GLU* 3.7 7.4 - - - +
14A LYS* 1.3 76.2 - - - +
16A TRP* 1.3 64.5 + - - +
18A LYS* 3.2 9.7 + - - +
19A ASP* 3.0 24.0 + - - +
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Residues in contact with TRP 16 (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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12A GLU 2.9 18.4 + - - +
13A ARG* 3.7 6.5 - - - +
15A ALA* 1.3 77.2 - - - +
17A ARG* 1.3 67.5 + - + +
19A ASP 3.2 14.3 + - - +
20A HIS* 2.8 66.3 + + + -
21A PRO* 4.0 8.1 - - + -
24A PHE* 3.7 31.9 - + + -
25A VAL* 4.0 1.4 - - - +
26A ALA* 3.4 49.6 + - + +
27A VAL* 5.6 1.5 - - + +
41A TRP* 4.9 4.7 - + + -
109A ILE* 4.3 13.7 - - + -
110A LYS* 3.9 31.6 - - + -
113A LEU* 3.7 18.6 - - + -
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Residues in contact with ARG 17 (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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13A ARG* 2.9 69.1 + - + +
14A LYS* 3.7 6.7 - - - +
16A TRP* 1.3 83.8 - - + +
18A LYS* 1.3 62.4 + - - +
19A ASP* 3.6 0.3 + - - -
20A HIS* 4.6 8.8 + - - -
27A VAL* 6.0 4.4 - - + +
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Residues in contact with LYS 18 (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 LYS 3.0 18.8 + - - +
15A ALA* 3.5 9.0 - - - +
16A TRP 3.2 0.2 - - - -
17A ARG* 1.3 79.8 - - - +
19A ASP* 1.3 67.9 + - + +
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Residues in contact with ASP 19 (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 3.0 15.7 + - - +
16A TRP* 3.2 8.2 + - - +
17A ARG 4.6 0.2 - - - -
18A LYS* 1.3 86.6 - - + +
20A HIS* 1.3 72.1 + - - +
110A LYS* 4.6 17.0 + - - +
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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