Contacts of the helix formed by residues 6 - 20 (chain A) in PDB entry 1N8T
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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA 2.7 13.6 + - - +
3A LEU* 2.9 18.1 + - - +
5A ARG* 1.3 71.2 - - - +
7A PRO* 1.3 67.2 - - - +
8A GLN* 2.7 29.9 + - - +
9A PHE* 2.9 17.9 + - + +
10A GLN* 2.9 27.8 + - - +
70A LEU* 3.6 6.2 - - - +
73A SER* 2.3 45.9 + - - -
74A ARG* 3.9 13.4 - - - +
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Residues in contact with PRO 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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5A ARG 3.4 6.5 - - - +
6A ASN* 1.3 92.9 - - - +
8A GLN* 1.3 80.6 + - - +
10A GLN* 3.3 16.8 + - - +
11A LYS* 3.0 24.8 + - - +
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Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 2.7 16.7 + - - +
7A PRO* 1.3 88.0 - - - +
9A PHE* 1.3 63.4 + - - +
11A LYS* 3.3 7.9 + - - +
12A LEU* 3.1 23.0 + - - +
66A MET* 5.0 3.3 - - - +
69A ASP* 3.9 27.1 - - + +
70A LEU* 3.8 18.9 - - + +
73A SER* 3.2 30.1 + - - +
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Residues in contact with PHE 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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3A LEU* 3.2 62.8 - - + +
4A THR* 3.9 23.1 - - + -
6A ASN* 2.9 9.8 + - - +
8A GLN* 1.3 77.6 - - - +
10A GLN* 1.3 59.1 + - + +
12A LEU* 3.3 13.4 + - + +
13A GLN* 3.0 65.4 + - + +
70A LEU* 3.6 20.7 - - + +
324A ILE* 5.0 2.7 - - + -
328A ASN* 3.8 27.8 - - + -
372A HIS* 4.9 7.6 - - + -
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Residues in contact with GLN 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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4A THR 3.9 20.4 + - - +
5A ARG* 4.2 8.0 + - - +
6A ASN 2.9 17.4 + - - +
7A PRO* 3.6 18.9 - - - +
8A GLN 3.2 0.4 - - - -
9A PHE* 1.3 79.3 - - + +
11A LYS* 1.3 56.5 + - - +
13A GLN* 3.1 6.9 + - - +
14A GLN* 2.8 31.9 + - - +
17A ARG* 4.9 2.2 + - - +
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Residues in contact with LYS 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 PRO 3.0 17.0 + - - +
8A GLN* 3.9 7.4 - - - +
10A GLN* 1.3 72.9 - - - +
12A LEU* 1.3 61.1 + - - +
14A GLN* 3.5 17.3 - - + +
15A TRP* 2.8 32.3 + - + +
62A GLU* 5.7 3.6 - - - -
66A MET* 3.8 31.9 - - + +
69A ASP* 4.7 10.1 + - - +
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Residues in contact with LEU 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 GLN 3.1 13.4 + - - +
9A PHE* 3.3 14.8 - - + +
11A LYS* 1.3 78.9 - - - +
13A GLN* 1.3 62.1 + - - +
15A TRP* 3.4 0.9 + - - +
16A HIS* 3.0 23.9 + - - +
63A VAL* 4.7 1.8 - - + +
66A MET* 3.9 40.8 - - + +
67A LEU* 3.7 28.5 - - + -
70A LEU* 4.6 14.6 - - + -
324A ILE* 5.0 5.6 - - + -
325A TRP* 3.3 30.5 - - + -
329A CYS* 3.7 23.3 - - - -
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Residues in contact with GLN 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 PHE* 3.0 47.9 + - + +
10A GLN* 3.1 8.6 + - - +
12A LEU* 1.3 75.0 - - - +
14A GLN* 1.3 65.7 - - - +
16A HIS* 3.2 4.6 + - - +
17A ARG* 2.9 42.3 + - - +
328A ASN 3.0 22.2 + - - -
329A CYS* 4.0 18.8 - - + +
372A HIS* 6.1 0.6 - - - +
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Residues in contact with GLN 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 GLN 2.8 19.7 + - - +
11A LYS* 3.5 21.2 - - + +
13A GLN* 1.3 71.6 - - - +
15A TRP* 1.3 67.5 + - - +
17A ARG* 3.2 30.1 + - - +
18A GLU* 3.2 43.8 + - - +
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Residues in contact with TRP 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 LYS* 2.8 21.2 + - + +
12A LEU 3.6 3.8 - - - +
14A GLN* 1.3 80.6 - - + +
16A HIS* 1.3 58.3 + - - +
18A GLU* 2.9 6.7 + - - +
19A HIS* 2.7 76.9 + + + -
20A GLY 4.0 1.8 - - - -
22A GLU* 5.0 4.3 - - - -
23A LEU* 4.0 27.1 - - + -
60A THR* 4.5 7.0 - - + -
62A GLU* 3.3 35.0 + - - -
63A VAL* 3.7 26.7 - - + -
66A MET* 3.3 29.6 - - + -
325A TRP* 4.0 11.9 - + - -
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Residues in contact with HIS 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 LEU 3.0 16.9 + - - +
13A GLN 3.6 4.2 + - - +
15A TRP* 1.3 85.3 - - - +
17A ARG* 1.3 65.4 + - - +
20A GLY* 2.8 29.5 + - - +
21A SER 4.4 2.2 + - - -
325A TRP* 3.8 17.5 - + + -
329A CYS* 3.2 40.0 + - + +
330A PHE* 3.4 52.3 - + - -
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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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10A GLN* 4.9 1.6 + - - +
13A GLN* 2.9 26.8 + - - +
14A GLN* 3.2 50.3 - - - +
15A TRP 3.2 0.2 - - - -
16A HIS* 1.3 82.5 + - - +
18A GLU* 1.3 64.9 + - + +
20A GLY 5.0 0.2 + - - -
21A SER 5.9 0.2 + - - -
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Residues in contact with GLU 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 GLN* 3.2 37.2 + - - +
15A TRP* 2.9 7.8 + - - +
17A ARG* 1.3 82.7 - - + +
19A HIS* 1.3 85.5 + - + +
22A GLU* 4.7 1.9 - - - +
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Residues in contact with HIS 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 TRP* 2.7 64.6 + + + -
18A GLU* 1.3 100.1 + - + +
20A GLY* 1.3 59.1 + - - +
21A SER 3.4 2.2 - - - -
22A GLU* 2.8 63.2 + - - +
23A LEU* 3.7 2.8 + - - +
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Residues in contact with GLY 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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15A TRP* 4.0 1.7 - - - -
16A HIS* 2.8 45.9 + - - +
17A ARG 5.0 0.2 + - - -
19A HIS* 1.3 71.7 - - - +
21A SER* 1.3 61.1 + - - +
22A GLU 3.2 1.2 + - - -
23A LEU* 3.3 30.2 + - - +
58A LEU* 5.8 0.2 - - - +
330A PHE* 3.9 16.2 - - - -
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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