Contacts of the helix formed by residues 4 - 21 (chain A) in PDB entry 6H5H
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 ASN 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A THR* 3.1 4.7 - - + +
3A LEU* 1.3 76.8 - - - +
5A GLY* 1.3 64.8 + - - +
6A ALA* 3.1 3.4 - - - -
7A LEU* 2.9 23.7 + - + +
8A VAL* 2.9 23.7 + - + +
37A LEU* 3.0 36.7 + - + +
40A TYR* 3.8 13.3 + - - -
42A HIS 2.9 22.3 + - - -
43A LYS* 3.4 5.5 - - - +
44A ILE* 3.0 35.7 + - - +
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Residues in contact with GLY 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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1A GLU 5.6 3.1 - - - -
2A THR* 2.8 23.9 + - - -
3A LEU 3.4 0.6 - - - -
4A ASN* 1.3 75.9 - - - +
6A ALA* 1.3 63.0 + - - +
8A VAL* 3.0 13.9 + - - +
9A ASN* 2.9 30.6 + - - +
38A ASP* 5.1 2.5 - - - -
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Residues in contact with ALA 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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3A LEU 4.9 3.3 + - - +
4A ASN 3.0 1.5 + - - -
5A GLY* 1.3 75.7 - - - +
7A LEU* 1.3 64.9 + - + +
9A ASN* 3.2 14.1 + - - +
10A MET* 3.2 19.1 + - - +
67A PHE* 4.1 27.6 - - + -
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU 5.9 0.2 - - - +
4A ASN* 2.9 29.2 + - + +
6A ALA* 1.3 76.9 - - + +
8A VAL* 1.3 57.9 + - + +
10A MET* 3.1 14.4 + - + +
11A LEU* 2.9 39.6 + - + +
37A LEU* 5.5 4.9 - - + -
43A LYS* 6.1 2.7 - - + +
44A ILE* 4.8 13.2 - - + +
64A ILE* 4.1 32.5 - - + +
67A PHE* 3.1 49.8 - - + -
68A LEU* 5.3 5.8 - - + -
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Residues in contact with VAL 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 ASN 2.9 20.5 + - - +
5A GLY* 3.0 12.5 + - - +
7A LEU* 1.3 76.1 - - - +
9A ASN* 1.3 65.7 + - - +
11A LEU* 3.1 11.5 + - - +
12A LYS* 3.0 21.5 + - + +
34A ALA* 3.7 36.9 - - + +
37A LEU* 4.3 8.3 - - + -
38A ASP* 4.2 21.5 - - + +
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Residues in contact with ASN 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 GLY 2.9 24.2 + - - +
6A ALA* 3.2 10.4 + - - +
8A VAL* 1.3 81.3 - - - +
10A MET* 1.3 62.4 + - - +
12A LYS* 3.0 21.2 + - - +
13A GLU* 3.1 12.0 + - - +
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Residues in contact with MET 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 ALA 3.2 8.4 + - - +
7A LEU* 3.1 20.1 + - + +
9A ASN* 1.3 77.5 - - - +
11A LEU* 1.3 68.5 + - + +
13A GLU* 3.1 19.3 + - - +
14A GLU* 3.0 31.9 + - + +
63A LYS* 3.5 42.2 - - + +
64A ILE* 4.4 2.0 - - + +
66A GLU* 6.2 0.9 - - - +
67A PHE* 3.5 38.4 - - + -
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Residues in contact with LEU 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 LEU* 2.9 21.3 + - + +
8A VAL* 3.3 11.0 - - - +
10A MET* 1.3 88.1 - - + +
12A LYS* 1.3 56.5 + - - +
14A GLU* 3.0 9.4 + - + +
15A GLY* 2.8 26.0 + - - -
30A TYR* 4.0 23.9 - - + +
31A TYR* 5.0 0.4 - - - -
33A ALA 4.6 0.4 - - - -
34A ALA* 3.8 26.0 - - + +
37A LEU* 3.2 34.3 - - + -
60A ILE* 3.5 31.2 - - + +
63A LYS* 5.2 4.0 - - + -
64A ILE* 5.4 3.8 - - + -
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Residues in contact with LYS 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 VAL* 3.0 12.0 + - + +
9A ASN* 3.3 14.1 - - - +
11A LEU* 1.3 75.8 - - - +
13A GLU* 1.3 63.7 + - - +
15A GLY* 3.2 2.1 + - - -
16A ASN* 3.0 37.3 + - - +
31A TYR* 4.1 25.0 - - + -
34A ALA* 5.3 0.6 - - - +
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Residues in contact with GLU 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 ASN 3.1 10.9 + - - +
10A MET* 3.3 20.8 - - - +
12A LYS* 1.3 76.7 - - - +
14A GLU* 1.3 69.0 + - + +
16A ASN* 3.2 13.0 + - + +
17A LYS* 3.0 22.1 + - + +
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Residues in contact with GLU 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 MET* 3.0 27.4 + - + +
11A LEU* 3.4 11.0 - - + +
13A GLU* 1.3 83.1 - - - +
15A GLY* 1.3 63.9 + - - +
17A LYS* 3.1 33.9 + - - +
18A ALA* 3.0 22.0 + - - +
30A TYR* 4.2 26.1 + - + -
63A LYS* 3.8 41.5 + - + +
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Residues in contact with GLY 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 LEU 2.8 13.6 + - - -
12A LYS 3.2 4.0 + - - -
14A GLU* 1.3 76.3 - - - +
16A ASN* 1.3 62.2 + - - +
18A ALA 3.1 1.9 + - - -
19A LEU* 3.0 19.1 + - - +
27A ALA* 3.2 27.8 - - - +
30A TYR* 4.0 8.7 - - - -
31A TYR* 3.7 16.2 - - - -
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Residues in contact with ASN 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 LYS* 3.0 34.0 + - - +
13A GLU* 3.2 12.0 + - + +
15A GLY* 1.3 75.3 - - - +
17A LYS* 1.3 58.1 + - - +
19A LEU* 3.2 13.4 + - + +
20A SER* 2.8 32.0 + - - +
31A TYR* 2.9 20.3 + - - -
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Residues in contact with LYS 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 GLU* 3.0 13.4 + - + +
14A GLU* 3.1 32.3 + - - +
16A ASN* 1.3 76.1 - - - +
18A ALA* 1.3 63.0 + - - +
20A SER* 2.9 21.2 + - - -
21A VAL* 3.1 21.9 + - + +
30A TYR* 6.2 0.4 - - - -
63A LYS* 5.0 7.9 - - - +
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Residues in contact with ALA 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 GLU 3.0 11.9 + - - +
15A GLY 3.5 8.3 - - - +
17A LYS* 1.3 77.7 - - - +
19A LEU* 1.3 55.3 + - - +
21A VAL* 2.8 18.2 - - - +
23A ASN* 2.7 48.7 + - + +
26A ASP* 4.0 11.2 - - + -
27A ALA* 3.6 14.6 - - - +
30A TYR* 4.2 6.7 - - + -
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Residues in contact with LEU 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 GLY 3.0 12.9 + - - +
16A ASN* 3.4 15.7 - - - +
18A ALA* 1.3 77.6 - - - +
20A SER* 1.3 56.7 + - - +
22A GLY* 2.9 20.1 + - - +
23A ASN 4.5 2.7 - - - +
24A ILE* 3.7 35.4 - - + -
27A ALA* 4.1 7.5 - - + +
31A TYR* 5.5 3.1 - - - +
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Residues in contact with SER 20 (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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16A ASN* 2.8 22.2 + - - +
17A LYS* 3.2 15.4 - - - -
19A LEU* 1.3 76.1 - - - +
21A VAL* 1.3 61.1 + - - +
22A GLY 3.5 0.5 + - - -
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 3.1 17.5 + - + +
18A ALA* 2.8 30.7 - - - +
20A SER* 1.3 79.4 - - - +
22A GLY* 1.3 58.3 + - - +
23A ASN* 3.6 16.1 - - + +
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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