Contacts of the helix formed by residues 2 - 18 (chain B) in PDB entry 3NYN
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 GLU 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B ACE 1.3 71.0 - - - +
3B LEU* 1.3 65.9 + - - +
4B GLU 3.3 1.6 - - - -
5B ASN* 3.5 28.2 + - + +
6B ILE* 3.4 32.1 + - + +
476B ASP* 4.9 5.5 - - - +
478B LEU* 5.4 0.4 - - - -
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Residues in contact with LEU 3 (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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1B ACE 3.4 2.6 - - + +
2B GLU* 1.3 76.9 - - - +
4B GLU* 1.3 65.4 + - - +
6B ILE* 3.1 13.1 + - + +
7B VAL* 2.9 42.9 + - + +
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Residues in contact with GLU 4 (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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1B ACE 4.3 11.3 + - - +
3B LEU* 1.3 80.3 - - - +
5B ASN* 1.3 60.3 + - - +
7B VAL* 3.8 7.1 - - - +
8B ALA* 3.3 25.1 + - + +
477B VAL* 4.9 12.2 - - + +
478B LEU* 4.3 25.4 - - + +
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Residues in contact with ASN 5 (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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2B GLU* 3.5 28.9 + - + +
3B LEU 3.1 0.8 - - - -
4B GLU* 1.3 77.0 - - - +
6B ILE* 1.3 66.4 + - + +
8B ALA* 4.1 0.5 - - - +
9B ASN* 3.1 32.6 + - - +
476B ASP* 3.3 40.9 + - + +
477B VAL* 4.0 9.1 + - - +
478B LEU* 3.5 37.2 + - - +
479B ASP* 4.2 11.1 + - - -
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Residues in contact with ILE 6 (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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2B GLU* 3.4 30.0 + - + +
3B LEU* 3.1 12.4 + - + +
5B ASN* 1.3 76.2 - - + +
7B VAL* 1.3 59.0 + - + +
9B ASN* 4.1 4.6 - - - +
10B THR* 2.4 41.9 + - - +
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Residues in contact with VAL 7 (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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3B LEU* 2.9 41.5 + - + +
4B GLU* 3.8 8.5 - - + +
5B ASN 3.2 0.2 - - - -
6B ILE* 1.3 74.5 - - - +
8B ALA* 1.3 64.2 + - - +
10B THR* 2.9 5.9 + - - -
11B VAL* 2.8 43.5 + - + +
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Residues in contact with ALA 8 (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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4B GLU* 3.3 16.1 + - + +
5B ASN 4.2 0.4 - - - +
7B VAL* 1.3 83.3 - - + +
9B ASN* 1.3 62.3 + - - +
11B VAL* 3.4 8.3 + - - +
12B LEU* 3.2 23.7 + - - +
190B ARG* 3.7 30.5 - - + +
477B VAL* 3.7 16.2 - - + -
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Residues in contact with ASN 9 (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 ASN 3.1 20.6 + - - +
6B ILE* 4.1 5.8 - - - +
8B ALA* 1.3 77.5 - - - +
10B THR* 1.3 57.4 + - - +
13B LEU* 3.0 36.2 + - + +
190B ARG* 3.1 27.5 + - - +
472B ILE* 3.6 28.0 - - + +
476B ASP* 3.6 26.2 + - - +
477B VAL* 4.5 2.3 - - - +
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Residues in contact with THR 10 (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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6B ILE* 2.4 35.8 + - - +
7B VAL* 2.9 4.8 + - - -
9B ASN* 1.3 76.1 - - - +
11B VAL* 1.3 66.2 + - - +
13B LEU* 3.8 11.0 - - + +
14B LYS* 3.1 29.4 + - + +
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Residues in contact with VAL 11 (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* 2.8 35.0 + - + +
8B ALA* 3.5 10.5 - - - +
10B THR* 1.3 75.8 - - - +
12B LEU* 1.3 67.2 + - - +
14B LYS* 2.9 16.7 + - - +
15B ALA* 3.2 11.9 + - + +
189B TYR* 4.4 29.6 - - + -
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Residues in contact with LEU 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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8B ALA 3.2 11.9 + - - +
9B ASN 4.0 2.9 - - - +
11B VAL* 1.3 81.9 - - + +
13B LEU* 1.3 63.1 + - - +
14B LYS 3.2 0.2 + - - -
15B ALA* 3.4 5.6 + - - +
16B ARG* 3.1 44.1 + - + +
189B TYR* 4.7 7.0 - - + -
190B ARG* 3.8 30.5 - - + -
192B LEU* 4.5 11.9 - - + -
202B ALA* 3.9 28.0 - - + -
211B MET* 4.3 18.6 - - + -
265B LEU* 5.1 4.9 - - + -
472B ILE* 4.2 16.6 - - + -
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Residues in contact with LEU 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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9B ASN* 3.0 26.6 + - + +
10B THR* 3.8 12.1 - - + +
12B LEU* 1.3 77.7 - - - +
14B LYS* 1.3 60.8 + - - +
16B ARG* 3.9 16.1 - - - +
17B GLU* 3.4 23.0 + - - +
469B PRO 4.1 6.3 - - - +
470B GLN* 3.1 47.1 - - + +
472B ILE* 4.1 18.2 - - + +
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Residues in contact with LYS 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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10B THR* 3.1 19.4 + - + +
11B VAL* 2.9 11.7 + - - +
13B LEU* 1.3 75.8 - - - +
15B ALA* 1.3 67.8 + - - +
17B GLU* 2.8 30.5 + - + +
18B GLY 2.9 15.3 + - - +
19B GLY* 5.2 8.3 - - - +
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Residues in contact with ALA 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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11B VAL* 3.2 8.2 + - + +
12B LEU* 3.8 7.6 - - - +
14B LYS* 1.3 78.2 - - - +
16B ARG* 1.3 61.7 + - - +
18B GLY 2.8 22.9 - - - +
19B GLY* 5.3 2.2 - - - -
189B TYR* 4.0 23.6 - - + +
204B GLN* 4.3 14.4 + - - +
211B MET* 3.9 22.8 - - + +
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Residues in contact with ARG 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 LEU* 3.1 39.6 + - + +
13B LEU* 3.9 16.9 - - - +
14B LYS 3.2 0.2 - - - -
15B ALA* 1.3 79.8 - - - +
17B GLU* 1.3 64.1 + - - +
18B GLY* 4.7 0.2 - - - -
192B LEU* 6.1 1.8 - - - +
211B MET* 4.0 11.5 - - - -
267B ASN* 3.5 56.7 + - - +
321B ASP* 5.7 0.9 - - - +
468B ASP 4.8 0.2 + - - -
469B PRO* 2.8 43.5 + - - +
471B ALA 3.1 24.4 + - - -
472B ILE* 4.5 9.3 - - - +
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Residues in contact with GLU 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 LEU 3.4 12.6 + - - +
14B LYS* 2.8 26.2 + - + +
16B ARG* 1.3 83.3 - - - +
18B GLY* 1.3 57.5 + - - +
470B GLN* 4.2 20.9 + - - +
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Residues in contact with GLY 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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14B LYS 2.9 8.3 + - - -
15B ALA* 2.8 23.4 - - - +
16B ARG 4.7 0.2 - - - -
17B GLU* 1.3 81.1 - - - +
19B GLY* 1.3 57.5 + - - -
21B GLY 6.2 0.4 - - - -
24B LYS* 4.7 9.2 - - - -
25B GLY* 4.3 13.6 + - - -
204B GLN* 5.1 0.7 + - - -
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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