Contacts of the helix formed by residues 2 - 19 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ACE 1.3 71.7 + - - +
3A LEU* 1.3 61.2 + - - +
4A GLU* 3.4 1.6 - - - +
5A ASN* 3.6 33.7 + - - +
6A ILE* 3.8 20.4 + - - +
478A LEU* 5.9 6.1 - - + -
479A ASP* 6.1 1.1 - - - -
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Residues in contact with LEU 3 (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 ACE 3.2 10.0 - - + +
2A GLU* 1.3 78.4 - - - +
4A GLU* 1.3 66.2 + - - +
6A ILE* 3.1 13.4 + - + -
7A VAL* 2.8 43.6 + - + +
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Residues in contact with GLU 4 (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 ACE 4.5 11.5 - - + +
2A GLU* 5.1 0.7 - - - -
3A LEU* 1.3 79.4 - - - +
5A ASN* 1.3 67.0 + - - +
7A VAL* 3.5 7.5 - - + +
8A ALA* 3.0 27.5 + - + +
477A VAL* 4.9 14.5 - - + +
478A LEU* 4.8 17.3 - - + +
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Residues in contact with ASN 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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2A GLU* 3.6 40.6 + - + +
3A LEU 3.2 0.2 - - - -
4A GLU* 1.3 81.5 - - - +
6A ILE* 1.3 65.4 + - + +
8A ALA* 3.5 1.0 + - - +
9A ASN* 3.2 29.0 + - - +
476A ASP* 3.6 36.9 + - + +
477A VAL* 3.9 11.6 + - - +
478A LEU* 3.6 31.8 + - - +
479A ASP* 4.8 6.5 + - - -
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Residues in contact with ILE 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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2A GLU 3.8 14.4 - - - +
3A LEU* 3.1 13.9 + - + +
5A ASN* 1.3 74.6 - - + +
7A VAL* 1.3 62.1 + - - +
9A ASN* 3.5 6.4 + - + +
10A THR* 2.6 41.3 + - - +
476A ASP* 5.9 1.1 - - - +
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Residues in contact with VAL 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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3A LEU* 2.8 44.6 + - + +
4A GLU* 3.5 8.7 - - + +
6A ILE* 1.3 75.5 - - - +
8A ALA* 1.3 69.1 + - + +
10A THR* 2.9 16.8 + - - -
11A VAL* 3.0 24.6 + - + +
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Residues in contact with ALA 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 GLU* 3.0 16.4 + - + +
5A ASN 4.0 0.9 - - - +
7A VAL* 1.3 83.6 - - + +
9A ASN* 1.3 62.2 + - - +
11A VAL* 3.5 8.0 + - - +
12A LEU* 3.1 24.3 + - - +
189A TYR* 5.8 0.3 - - - -
190A ARG* 3.6 30.8 + - + +
477A VAL* 4.0 14.4 - - + -
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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 ASN 3.2 17.7 + - - +
6A ILE* 3.8 7.4 - - + +
7A VAL 3.1 0.6 - - - -
8A ALA* 1.3 79.0 - - - +
10A THR* 1.3 61.7 + - - +
12A LEU* 3.5 0.6 + - - -
13A LEU* 3.1 25.3 + - + +
190A ARG* 3.2 25.7 + - - +
472A ILE* 3.4 41.6 - - + +
474A CYS 6.0 0.2 + - - -
476A ASP* 4.0 20.5 + - - +
477A VAL* 4.8 1.4 - - - +
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Residues in contact with THR 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 ILE* 2.6 32.3 + - - +
7A VAL* 2.9 5.5 + - - -
9A ASN* 1.3 73.8 - - - +
11A VAL* 1.3 67.7 + - - +
13A LEU* 3.5 8.8 + - + +
14A LYS* 3.1 24.8 + - + +
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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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7A VAL* 3.0 29.4 + - + +
8A ALA* 3.5 11.2 - - - +
10A THR* 1.3 75.2 - - - +
12A LEU* 1.3 65.6 + - - +
14A LYS* 2.9 18.8 + - - +
15A ALA* 3.0 11.3 + - - +
189A TYR* 3.4 31.6 - - + -
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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 ALA 3.1 14.5 + - - +
9A ASN 3.8 3.6 - - - +
11A VAL* 1.3 82.5 - - - +
13A LEU* 1.3 59.6 + - - +
15A ALA* 3.2 3.5 + - + +
16A ARG* 2.9 47.8 + - + +
189A TYR* 4.4 14.6 - - + -
190A ARG* 3.7 29.8 - - + -
192A LEU* 4.3 14.6 - - + -
202A ALA* 3.8 24.7 - - + -
211A MET* 5.2 9.6 - - - -
265A LEU* 5.4 4.5 - - + -
472A ILE* 4.1 19.5 - - + -
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Residues in contact with LEU 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 20.9 + - + +
10A THR* 3.9 9.2 - - + +
12A LEU* 1.3 79.7 - - - +
14A LYS* 1.3 58.0 + - - +
16A ARG* 3.5 22.7 + - - +
17A GLU* 2.8 32.4 + - - +
469A PRO 3.7 18.6 - - - +
470A GLN* 3.4 45.1 - - - +
472A ILE* 3.9 19.7 - - + -
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Residues in contact with LYS 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 THR* 3.1 14.3 + - + +
11A VAL* 2.9 12.9 + - - +
13A LEU* 1.3 75.1 - - - +
15A ALA* 1.3 62.1 + - - +
17A GLU* 2.9 34.7 + - + +
18A GLY 3.1 7.1 + - - -
19A GLY* 3.6 22.5 + - - +
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Residues in contact with ALA 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 3.0 6.2 + - - +
12A LEU* 3.5 9.0 - - + +
14A LYS* 1.3 76.7 - - - +
16A ARG* 1.3 62.7 + - - +
17A GLU 3.3 0.3 + - - -
18A GLY* 3.8 6.4 + - - -
19A GLY* 3.8 14.4 + - - +
189A TYR* 3.2 41.1 - - + +
204A GLN* 4.3 10.4 + - - +
211A MET* 3.9 19.9 - - - +
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Residues in contact with ARG 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* 2.9 41.0 + - + +
13A LEU* 3.5 18.7 - - - +
15A ALA* 1.3 76.1 - - - +
17A GLU* 1.3 64.1 + - - +
192A LEU* 5.9 2.2 - - - +
211A MET* 4.2 13.9 - - + -
265A LEU* 5.5 1.2 - - + +
267A ASN* 3.6 57.8 + - - +
321A ASP* 5.9 0.7 - - - +
469A PRO* 3.1 27.2 + - - +
471A ALA 2.9 27.7 + - - -
472A ILE* 4.6 8.4 - - - +
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Residues in contact with GLU 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 LEU* 2.8 16.5 + - - +
14A LYS* 2.9 24.5 + - + +
16A ARG* 1.3 80.6 - - - +
18A GLY* 1.3 59.1 + - - +
470A GLN* 3.1 32.6 + - - +
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Residues in contact with GLY 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 LYS 3.1 0.4 + - - -
15A ALA 3.8 2.0 + - - -
17A GLU* 1.3 83.1 - - - +
19A GLY* 1.3 68.5 + - - +
20A GLY 3.1 4.0 + - - -
21A GLY* 3.6 18.9 + - - +
23A ARG 4.2 2.4 - - - +
24A LYS* 4.5 8.8 - - - +
25A GLY 4.5 4.7 - - - -
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Residues in contact with GLY 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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14A LYS* 3.6 33.5 + - - +
15A ALA* 3.8 14.0 + - - -
18A GLY* 1.3 73.6 - - - +
20A GLY* 1.3 58.1 + - - -
21A GLY 4.2 0.5 + - - -
25A GLY* 4.0 20.3 - - - +
204A GLN* 5.3 1.1 - - - -
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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