Contacts of the helix formed by residues 7 - 21 (chain A) in PDB entry 4II9
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 ASP 7 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASN* 3.0 27.7 + - + +
5A LEU 3.4 0.8 - - - -
6A ASN* 1.3 76.9 - - - +
8A PRO* 1.4 66.3 - - - +
9A GLN* 3.1 19.1 + - - +
10A ALA* 3.2 22.4 + - + +
11A VAL* 3.0 24.4 + - - +
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Residues in contact with PRO 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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5A LEU 5.7 0.9 - - - +
6A ASN 3.2 12.3 - - - +
7A ASP* 1.4 84.5 - - - +
9A GLN* 1.3 58.0 + - - +
11A VAL* 3.6 8.7 - - + +
12A GLU* 2.8 31.0 + - - +
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Residues in contact with GLN 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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7A ASP* 3.1 9.0 + - - +
8A PRO* 1.3 75.7 - - - +
10A ALA* 1.3 65.9 + - - +
12A GLU* 3.3 5.5 + - - +
13A ARG* 3.0 24.3 + - + +
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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
----------------------------------------------------------
3A LEU* 3.6 18.8 - - + +
4A ASN* 4.4 5.4 - - + +
7A ASP* 3.2 30.5 + - + +
9A GLN* 1.3 77.6 - - - +
11A VAL* 1.3 61.6 + - - +
13A ARG* 3.2 11.2 + - - +
14A TYR* 2.9 30.1 + - - +
45A TYR* 6.0 2.7 - - + +
53A ILE* 5.6 0.3 - - - +
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Residues in contact with VAL 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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3A LEU* 4.1 14.4 - - + -
4A ASN 3.8 9.4 - - - +
5A LEU* 3.8 30.7 - - + +
7A ASP 3.0 21.0 + - - +
8A PRO* 3.6 9.2 - - + +
10A ALA* 1.3 76.5 - - - +
12A GLU* 1.3 54.1 + - - +
14A TYR* 3.2 4.4 + - - +
15A GLU* 2.8 40.0 + - + +
30A LEU* 3.7 16.6 - - + -
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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 PRO 2.8 18.1 + - - +
9A GLN* 3.9 5.6 - - - +
11A VAL* 1.3 77.0 - - + +
13A ARG* 1.4 59.1 + - - +
15A GLU* 3.3 2.6 + - - +
16A GLU* 2.9 34.5 + - + +
19A ARG* 2.9 42.2 + - - -
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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
----------------------------------------------------------
9A GLN* 3.0 17.7 + - + +
10A ALA* 3.2 11.5 + - - +
12A GLU* 1.4 75.0 - - - +
14A TYR* 1.3 62.6 + - - +
16A GLU* 3.4 7.0 + - + +
17A PHE* 3.1 18.7 + - - +
45A TYR* 3.3 30.1 + - - -
47A GLU* 2.9 21.7 + - - -
51A GLY 2.8 28.9 + - - -
52A ALA* 4.5 1.2 - - - +
53A ILE* 3.7 26.6 - - + +
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Residues in contact with TYR 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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3A LEU* 3.8 16.4 - - + -
10A ALA 2.9 16.2 + - - +
11A VAL 3.5 3.6 - - - +
13A ARG* 1.3 77.2 - - - +
15A GLU* 1.3 62.7 + - - +
17A PHE* 3.3 5.4 + - - +
18A MET* 3.0 46.5 + - + +
28A GLN 4.5 0.9 - - - -
30A LEU* 3.6 29.8 - - + -
43A ASP* 3.5 14.3 - - + +
44A VAL 3.6 22.0 - - - -
45A TYR* 4.1 21.1 - + + -
53A ILE* 3.7 12.3 - - + +
56A ALA* 3.7 9.0 - - + -
57A MET 3.2 22.7 + - - -
58A SER* 2.7 31.4 + - - -
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Residues in contact with GLU 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 VAL* 2.8 30.3 + - + +
12A GLU* 3.7 6.7 - - - +
14A TYR* 1.3 72.1 - - - +
16A GLU* 1.3 61.4 + - - +
18A MET* 3.2 4.3 + - - +
19A ARG* 2.8 71.6 + - - +
29A ASP* 2.5 31.0 - - - +
30A LEU* 2.8 45.4 + - + +
31A GLY 5.1 0.2 - - - -
248A TYR* 5.0 0.7 - - - -
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Residues in contact with GLU 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 22.0 + - + +
13A ARG* 3.6 8.3 - - + +
14A TYR 3.2 0.2 - - - -
15A GLU* 1.3 75.5 - - - +
17A PHE* 1.3 63.5 + - - +
19A ARG* 3.8 16.8 + - - +
20A GLN* 2.8 54.7 + - + +
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Residues in contact with PHE 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 3.1 11.1 + - - +
14A TYR* 3.5 7.4 - - - +
15A GLU 3.2 0.2 - - - -
16A GLU* 1.3 81.7 - - - +
18A MET* 1.3 66.6 + - - +
20A GLN* 3.9 1.9 - - - +
21A SER* 3.1 32.3 + - - -
53A ILE* 3.4 47.1 - - + -
54A ILE 3.6 15.5 - - - -
55A ALA 3.9 0.7 - - - -
56A ALA* 3.8 21.8 - - + -
78A VAL* 3.5 42.4 - - + -
402A GOL 3.7 18.2 - - - -
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Residues in contact with MET 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 TYR* 3.0 43.4 + - + +
15A GLU* 3.6 11.4 - - - +
17A PHE* 1.3 84.3 - - + +
19A ARG* 1.3 63.1 - - - +
20A GLN 3.3 0.7 + - - -
21A SER* 3.5 8.5 + - - +
24A GLY* 3.7 20.5 - - - -
25A GLN 6.0 0.2 - - - -
28A GLN* 3.5 29.2 - - + +
29A ASP* 4.7 2.0 - - - +
56A ALA* 3.5 26.9 - - + -
58A SER* 3.5 2.2 - - - +
78A VAL* 3.4 39.3 - - + -
248A TYR* 3.4 20.7 - - + +
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Residues in contact with ARG 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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12A GLU* 2.9 42.4 + - - -
15A GLU* 2.8 50.8 + - - +
16A GLU* 3.8 20.6 + - - +
18A MET* 1.3 72.9 - - - +
20A GLN* 1.3 73.7 + - - +
21A SER 4.8 2.1 - - - +
29A ASP* 4.4 1.1 + - - +
248A TYR* 3.8 24.2 - - + +
249A GLY* 4.9 11.3 + - - -
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 2.8 45.7 + - - +
17A PHE* 3.9 2.7 - - - +
19A ARG* 1.3 93.3 + - - +
21A SER* 1.4 64.9 + - - +
22A PRO* 3.6 5.7 - - - +
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Residues in contact with SER 21 (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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17A PHE* 3.1 29.3 + - - -
18A MET 3.5 4.3 + - - +
19A ARG 4.8 0.3 - - - +
20A GLN* 1.4 78.2 - - - +
22A PRO* 1.3 73.8 - - - +
23A TYR* 3.0 22.2 + - - +
24A GLY* 3.1 12.9 + - - -
78A VAL* 3.5 27.4 - - - +
249A GLY* 4.3 10.2 - - - -
402A GOL 4.9 1.7 + - - -
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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