Contacts of the helix formed by residues 6 - 19 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ASP 5.2 2.7 + - - +
3C GLU 3.7 4.1 + - - +
5C VAL* 1.3 84.0 - - + +
7C THR* 1.3 55.3 + - - +
8C LYS 2.7 4.6 + - - -
9C GLU* 2.6 51.2 + - + +
10C LEU* 3.1 25.0 + - + +
13C TRP* 4.8 20.9 - + - -
30C SER* 5.6 6.3 - - - -
34C LYS* 3.2 52.3 - - + -
105C VAL* 5.2 0.9 - - + -
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Residues in contact with THR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A TYR* 4.2 25.0 + - + +
3C GLU* 3.6 17.3 + - - +
4C LYS* 5.0 2.2 - - - -
6C PHE* 1.3 77.8 - - - +
8C LYS* 1.3 59.0 + - - +
9C GLU 3.3 0.6 + - - -
10C LEU* 4.2 11.0 - - - +
11C ASP* 3.5 21.8 + - - +
106C ARG* 3.7 33.8 + - - +
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Residues in contact with LYS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A TYR* 5.7 5.2 - - - +
4C LYS* 3.5 30.4 + - + +
5C VAL 5.3 0.7 - - - -
6C PHE 2.7 4.4 + - - +
7C THR* 1.3 75.8 - - - +
9C GLU* 1.3 59.7 + - - +
11C ASP* 4.0 13.9 - - + +
12C GLN* 4.1 6.9 + - - +
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Residues in contact with GLU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL 4.6 6.2 + - - +
6C PHE* 2.6 44.9 + - + +
8C LYS* 1.3 72.3 - - - +
10C LEU* 1.3 65.2 + - - +
11C ASP 3.2 0.9 - - - -
12C GLN* 3.0 11.9 + - + +
13C TRP* 2.9 47.2 + - + +
27C GLN* 5.5 0.9 + - - -
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Residues in contact with LEU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PHE* 3.1 25.0 + - + +
7C THR* 4.6 5.8 - - - +
9C GLU* 1.3 74.8 - - - +
11C ASP* 1.3 56.0 + - - +
12C GLN 2.6 13.0 + - - -
13C TRP* 2.8 47.5 + - + +
14C ILE* 2.9 17.8 + - + +
31C LEU* 4.1 6.7 - - + -
102C ALA* 4.3 9.2 - - + +
105C VAL* 3.5 24.2 - - + +
106C ARG* 3.2 53.6 - - + +
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Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A TYR* 4.5 9.9 + - - -
7C THR 3.5 15.5 + - - +
8C LYS* 4.0 11.4 - - + +
10C LEU* 1.3 78.4 - - - +
12C GLN* 1.3 54.7 + - - +
14C ILE* 3.6 10.7 - - - +
15C GLU* 3.2 21.7 + - - +
106C ARG* 2.5 41.0 + - - +
107C TYR* 3.7 12.1 + - - -
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS 4.1 7.1 + - - +
9C GLU* 3.0 15.4 + - + +
10C LEU 2.6 5.1 + - - -
11C ASP* 1.3 73.0 - - - +
13C TRP* 1.3 79.3 + - - +
14C ILE 2.8 2.0 - - - -
15C GLU* 2.7 22.2 + - - +
16C GLN* 2.7 49.9 + - - +
27C GLN* 5.2 1.4 + - - -
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Residues in contact with TRP 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 4.8 16.4 - + - -
9C GLU* 2.9 38.7 + - + +
10C LEU* 2.8 41.0 + - + +
12C GLN* 1.3 86.5 - - - +
14C ILE* 1.3 54.8 + - + +
16C GLN* 3.2 3.4 - - - +
17C LEU* 2.8 41.7 + - + +
23C LEU* 3.6 30.5 - - + +
27C GLN* 2.4 52.3 - - + +
30C SER* 4.1 10.5 - - - -
31C LEU* 3.8 40.2 - - + -
34C LYS* 6.3 0.2 - - + -
102C ALA* 5.3 1.6 - - + -
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 2.9 21.4 + - + +
11C ASP* 3.6 9.2 - - - +
12C GLN 2.8 0.4 + - - -
13C TRP* 1.3 72.2 - - + +
15C GLU* 1.3 67.7 + - - +
16C GLN 3.0 1.6 - - - -
17C LEU* 2.9 10.7 + - - +
18C ASN* 2.8 39.2 + - - +
99C LEU* 4.7 9.4 - - + +
102C ALA* 4.1 23.6 - - + +
103C LEU* 4.3 17.3 - - + +
106C ARG* 4.0 33.2 - - + -
107C TYR* 4.6 10.3 - - + -
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASP 3.2 12.4 + - - +
12C GLN* 2.7 30.9 + - - +
14C ILE* 1.3 74.9 - - - +
16C GLN* 1.3 63.2 + - - +
18C ASN* 3.1 23.8 + - - +
19C GLU* 3.3 9.2 + - - +
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Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLN* 2.7 38.6 + - - +
13C TRP* 3.2 9.5 - - - +
15C GLU* 1.3 69.7 - - - +
17C LEU* 1.3 57.5 + - - +
18C ASN 2.9 4.3 - - - -
19C GLU* 2.8 27.8 + - - +
20C CYS 3.3 5.9 + - - -
21C LYS* 3.4 32.5 + - + +
22C GLN 2.9 26.9 + - - -
23C LEU* 4.0 12.9 - - + +
27C GLN* 4.8 6.8 + - - -
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TRP 2.8 24.9 + - - +
14C ILE 2.9 4.7 + - - +
16C GLN* 1.3 70.3 - - - +
18C ASN* 1.3 61.4 + - - +
20C CYS* 3.1 10.0 + - - -
21C LYS 3.3 20.2 - - - +
22C GLN* 3.9 4.7 - - - -
23C LEU* 3.7 21.3 - - + +
62C PHE* 3.2 19.9 - - - -
95C GLU* 4.2 9.8 - - + +
98C THR* 3.2 51.6 - - + +
99C LEU* 3.7 24.5 - - + -
102C ALA* 4.0 12.6 - - + -
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Residues in contact with ASN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 2.8 33.9 + - - +
15C GLU* 3.1 16.3 - - - +
16C GLN 2.8 0.2 + - - -
17C LEU* 1.3 76.0 - - - +
19C GLU* 1.3 56.7 + - - +
20C CYS 2.8 8.8 + - - -
62C PHE* 4.0 12.4 - - - -
66C MET* 3.9 27.4 - - - +
99C LEU* 4.7 9.0 - - - +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 3.3 7.0 + - + +
16C GLN* 2.8 14.0 + - - +
18C ASN* 1.3 75.6 - - - +
20C CYS* 1.3 69.4 + - - +
21C LYS* 4.4 33.0 + - + +
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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