Contacts of the helix formed by residues 11 - 24 (chain B) in PDB entry 3NT2
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 GLY 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B GLY 2.8 14.5 + - - -
10B THR* 1.3 74.7 - - - +
12B ALA* 1.3 66.4 + - - +
13B ILE 3.4 1.8 - - - -
14B GLY* 3.7 2.4 - - - -
15B LYS* 2.9 25.2 + - - +
73B THR 4.8 0.9 - - - -
400B NAI 3.6 32.9 - - - -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY* 1.3 73.0 - - - +
13B ILE* 1.3 62.6 + - + +
15B LYS* 3.3 22.4 + - - +
16B GLU* 3.4 16.2 + - - +
400B NAI 2.8 31.8 + - - +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 1.3 73.8 - - + +
14B GLY* 1.3 68.9 + - - +
16B GLU* 3.3 12.9 + - + +
17B HIS* 3.0 33.3 + - + +
20B ARG* 6.2 0.2 - - - +
73B THR* 3.8 25.8 - - + +
96B GLU* 3.9 22.0 - - + +
272B TRP* 4.3 14.4 - - + -
280B TYR* 4.8 13.0 - - + +
400B NAI 2.9 63.8 + - + +
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.6 3.6 - - - +
9B GLY 3.7 10.5 - - - -
10B THR* 4.5 1.3 - - - -
11B GLY* 3.4 7.2 + - - +
12B ALA 3.3 0.6 - - - -
13B ILE* 1.3 83.5 - - - +
15B LYS* 1.3 60.0 + - - +
17B HIS* 3.5 3.3 + - - +
18B ILE* 3.1 33.4 + - - +
73B THR* 3.5 25.5 + - - -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR 4.0 6.2 - - - +
11B GLY 2.9 23.3 + - - +
12B ALA* 3.5 14.7 - - - +
14B GLY* 1.3 77.2 - - - +
16B GLU* 1.3 57.6 + - + +
18B ILE* 3.2 10.1 + - - +
19B ASN* 2.9 27.7 + - - +
44B VAL* 3.9 31.4 - - + -
47B GLN* 5.8 5.8 - - + +
48B TYR* 3.8 28.5 + - + +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 3.4 12.0 + - - +
13B ILE* 3.3 20.5 + - + +
15B LYS* 1.3 77.3 - - + +
17B HIS* 1.3 60.2 + - - +
19B ASN* 3.1 17.0 + - - +
20B ARG* 2.9 51.2 + - - +
48B TYR* 4.7 7.0 + - - -
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.0 29.9 + - + +
14B GLY* 3.9 4.3 - - - +
16B GLU* 1.3 76.0 - - - +
18B ILE* 1.3 61.8 + - - +
20B ARG* 3.3 19.1 + - - +
21B ILE* 3.1 33.2 + - + +
71B LEU* 3.8 22.2 - - + -
73B THR* 4.1 20.2 - - + -
94B PHE* 4.0 7.4 - + - -
96B GLU* 2.6 30.6 + - - +
280B TYR* 4.5 16.6 - + - -
283B GLU* 4.6 1.6 - - - -
284B ILE* 3.7 31.7 - - + +
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 3.7 22.2 - - + -
10B THR* 4.1 8.1 - - + -
14B GLY 3.1 24.1 + - - +
15B LYS* 3.4 7.9 - - - +
17B HIS* 1.3 77.7 - - - +
19B ASN* 1.3 54.8 + - - +
21B ILE* 3.9 1.0 - - - +
22B THR* 2.5 42.5 + - - +
30B ILE* 4.1 10.9 - - + +
33B VAL* 3.8 28.3 - - + -
44B VAL* 3.9 20.0 - - + -
48B TYR* 3.9 17.5 - - + -
50B LEU* 3.6 25.4 - - + -
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS 2.9 15.9 + - - +
16B GLU* 3.1 18.3 + - - +
18B ILE* 1.3 79.4 - - - +
20B ARG* 1.3 62.3 + - - +
22B THR* 4.4 3.4 - - - -
23B ASN* 2.8 48.8 + - - +
24B LYS* 5.3 8.3 - - - +
48B TYR* 3.5 28.3 - - + +
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLU* 2.9 52.8 + - - +
17B HIS* 3.2 24.8 + - - +
19B ASN* 1.3 78.6 - - - +
21B ILE* 1.3 61.9 + - + +
24B LYS* 2.8 21.8 + - + -
25B LEU* 2.8 42.6 + - + -
277B VAL* 4.4 10.3 + - - +
280B TYR* 3.4 38.5 - - - +
281B ASP* 2.8 30.9 + - - +
284B ILE* 3.8 26.5 - - - -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 4.2 14.4 - - + -
17B HIS* 3.1 19.4 + - + +
18B ILE 4.0 2.2 - - - +
20B ARG* 1.3 80.7 - - + +
22B THR* 1.3 62.0 + - - +
25B LEU* 4.4 19.2 - - + +
28B ALA* 3.7 38.6 - - + +
29B GLU* 4.3 2.7 - - - +
30B ILE* 3.9 25.1 - - + -
71B LEU* 3.6 27.1 - - + -
284B ILE* 3.6 31.4 - - + -
288B ILE* 4.8 3.4 - - + -
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 2.5 26.8 + - - +
19B ASN* 3.9 3.6 - - - -
21B ILE* 1.3 80.3 - - - +
23B ASN* 1.3 77.2 + - - +
24B LYS 3.8 0.2 - - - -
25B LEU 5.8 0.7 - - - -
28B ALA 5.5 0.7 - - - -
29B GLU* 6.1 1.1 - - - +
30B ILE* 4.0 6.2 + - - +
48B TYR* 4.5 12.8 - - + +
50B LEU* 3.7 29.4 - - + +
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Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN* 2.8 38.4 + - - +
22B THR* 1.3 96.6 - - - +
24B LYS* 1.3 66.4 + - + +
48B TYR* 4.6 10.3 - - - +
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASN* 5.3 7.2 - - - +
20B ARG* 2.8 25.2 + - + +
22B THR 3.8 0.4 - - - -
23B ASN* 1.3 84.9 - - + +
25B LEU* 1.3 72.9 + - + +
277B VAL* 4.6 15.6 - - - +
281B ASP* 3.4 27.8 + - - +
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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