Contacts of the helix formed by residues 6 - 20 (chain F) in PDB entry 2NYM
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 PHE 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2F ASP 5.1 2.7 + - - +
3F GLU 3.7 4.5 + - - +
5F VAL* 1.3 84.9 - - + +
7F THR* 1.3 56.8 + - - +
8F LYS 2.6 16.5 + - - -
9F GLU* 2.7 35.1 + - + +
10F LEU* 3.1 23.0 + - + +
13F TRP* 4.9 18.6 - + - -
30F SER* 5.4 7.0 - - - -
34F LYS* 3.2 50.9 - - + -
105F VAL* 5.3 5.6 - - + -
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Residues in contact with THR 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577D TYR* 4.2 26.9 + - + -
3F GLU* 3.5 17.0 + - - +
4F LYS* 5.1 2.9 - - - -
6F PHE* 1.3 76.8 - - - +
8F LYS* 1.3 57.2 + - - +
10F LEU* 4.4 11.2 - - - +
11F ASP* 3.6 20.4 + - - +
106F ARG* 3.9 33.5 + - - +
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Residues in contact with LYS 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577D TYR* 5.8 1.6 - - - +
4F LYS* 3.4 30.8 + - + +
5F VAL 5.1 1.3 - - - -
6F PHE 2.6 7.6 + - - +
7F THR* 1.3 76.9 - - - +
9F GLU* 1.3 58.7 + - - +
11F ASP* 4.0 14.1 - - + +
12F GLN* 4.1 6.9 + - - +
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Residues in contact with GLU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL 4.8 5.6 + - - +
6F PHE* 2.7 34.6 + - + +
8F LYS* 1.3 78.1 - - - +
10F LEU* 1.3 65.3 + - - +
11F ASP 3.2 0.9 - - - -
12F GLN* 2.9 10.7 + - + +
13F TRP* 2.8 50.6 + - + +
27F GLN* 4.8 3.5 + - - -
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Residues in contact with LEU 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F PHE* 3.1 25.8 + - + +
7F THR* 4.8 6.1 - - - +
9F GLU* 1.3 75.2 - - - +
11F ASP* 1.3 57.0 + - - +
12F GLN 2.6 12.6 + - - -
13F TRP* 2.6 50.3 + - + +
14F ILE* 2.9 16.1 + - + +
31F LEU* 4.2 4.5 - - + -
102F ALA* 4.2 16.4 - - + +
105F VAL* 3.5 22.0 - - + +
106F ARG* 3.3 48.7 - - + +
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Residues in contact with ASP 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D TYR* 4.6 10.7 + - - -
7F THR 3.6 18.6 + - - +
8F LYS* 4.0 10.6 - - - +
10F LEU* 1.3 78.3 - - - +
12F GLN* 1.3 55.6 + - - +
14F ILE* 3.6 10.4 - - - +
15F GLU* 3.2 23.1 + - - +
106F ARG* 2.9 32.9 + - - +
107F TYR* 3.7 11.7 + - - -
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Residues in contact with GLN 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LYS 4.1 6.7 + - - +
9F GLU* 2.9 15.6 + - + +
10F LEU 2.6 4.6 + - - -
11F ASP* 1.3 74.3 - - - +
13F TRP* 1.3 84.7 + - - +
14F ILE 2.9 1.6 - - - -
15F GLU* 2.6 38.2 + - - +
16F GLN* 2.7 46.1 + - - +
27F GLN* 5.2 1.2 + - - -
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Residues in contact with TRP 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F PHE* 4.9 15.5 - + - -
9F GLU* 2.8 41.1 + - + +
10F LEU* 2.6 38.4 + - + +
12F GLN* 1.3 86.0 + - - +
14F ILE* 1.3 56.7 + - + +
16F GLN* 3.2 4.6 - - - +
17F LEU* 2.8 35.9 + - + +
23F LEU* 3.6 30.3 - - + +
27F GLN* 2.6 49.2 - - + +
30F SER* 4.3 9.4 - - - -
31F LEU* 3.6 45.8 - - + -
34F LYS* 6.3 0.4 - - + -
102F ALA* 5.3 1.3 - - + -
105F VAL* 6.0 0.4 - - + -
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Residues in contact with ILE 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 2.9 17.2 + - + +
11F ASP* 3.6 12.1 - - - +
12F GLN 2.8 0.4 + - - -
13F TRP* 1.3 71.8 - - + +
15F GLU* 1.3 68.2 + - - +
16F GLN 3.0 1.6 - - - -
17F LEU* 3.1 8.7 + - - +
18F ASN* 2.9 38.5 + - - +
99F LEU* 4.8 7.6 - - + -
102F ALA* 3.9 27.6 - - + +
103F LEU* 4.3 17.7 - - + +
106F ARG* 3.9 33.0 - - + -
107F TYR* 4.5 7.0 - - + -
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Residues in contact with GLU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ASP 3.2 12.9 + - - +
12F GLN* 2.6 37.9 + - - +
14F ILE* 1.3 78.7 - - - +
16F GLN* 1.3 57.6 + - - +
18F ASN* 3.3 18.3 + - - +
19F GLU* 3.4 10.4 + - - +
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Residues in contact with GLN 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLN* 2.7 35.8 + - - +
13F TRP* 3.2 11.1 - - - +
15F GLU* 1.3 73.5 - - - +
17F LEU* 1.3 64.9 + - - +
18F ASN 3.0 1.8 - - - -
19F GLU* 3.1 20.2 + - - +
20F CYS 3.3 0.2 + - - -
21F LYS* 3.2 38.8 + - + +
22F GLN 3.1 23.8 + - - -
23F LEU* 4.0 14.5 - - + +
27F GLN* 4.5 8.8 + - - +
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Residues in contact with LEU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TRP 2.8 23.4 + - - +
14F ILE 3.6 4.5 - - - +
16F GLN* 1.3 72.7 - - - +
18F ASN* 1.3 61.5 + - - +
20F CYS* 2.9 11.1 + - - -
21F LYS 3.4 18.6 - - - +
22F GLN* 4.1 4.0 - - - -
23F LEU* 3.7 17.0 - - + +
62F PHE* 3.1 19.1 - - - -
95F GLU* 4.4 8.8 - - + +
98F THR* 3.2 52.7 - - + +
99F LEU* 3.4 26.5 - - + -
102F ALA* 3.9 13.2 - - + -
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Residues in contact with ASN 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 2.9 33.1 + - - +
15F GLU* 3.3 13.6 - - - +
16F GLN 3.0 0.2 - - - -
17F LEU* 1.3 76.7 - - - +
19F GLU* 1.3 58.5 + - - +
20F CYS 2.7 10.7 + - - -
62F PHE* 3.6 15.5 - - - -
66F MET* 3.6 27.0 - - - +
99F LEU* 4.7 11.3 - - - +
103F LEU* 6.3 0.4 - - - +
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Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLU 3.4 8.0 + - - +
16F GLN* 3.1 13.9 + - - +
18F ASN* 1.3 77.5 - - - +
20F CYS* 1.3 67.4 + - - +
21F LYS* 4.1 33.6 + - + +
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Residues in contact with CYS 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LEU 2.9 13.1 + - - -
18F ASN 2.7 5.1 + - - -
19F GLU* 1.3 84.7 - - - +
21F LYS* 1.3 62.4 + - - +
22F GLN 4.1 0.4 - - - -
62F PHE* 3.7 35.0 - - + -
63F HIS* 4.4 11.7 - - - +
92F TYR* 4.3 21.3 - - - -
95F GLU* 4.1 23.9 - - - +
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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