Contacts of the strand formed by residues 13 - 18 (chain A) in PDB entry 1NB9
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 TYR 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A HIS* 3.5 15.2 + + + +
11A LEU* 3.8 6.7 - - + +
12A PRO* 1.3 73.6 - - - +
14A PHE* 1.3 69.5 + - - +
15A CYS* 3.7 30.6 - - + +
41A VAL 4.9 2.4 + - - -
44A ASN* 3.2 27.8 + - - +
45A LEU* 3.4 26.2 + - + -
46A PRO* 3.2 32.8 - - + -
49A ILE* 3.6 15.3 - - + -
104A VAL 3.7 1.2 - - - +
105A ALA* 3.5 1.2 - - - -
106A ILE* 2.8 42.0 + - + +
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Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO* 3.8 39.3 - - + -
13A TYR* 1.3 84.7 - - - +
15A CYS* 1.3 63.8 + - - +
104A VAL 3.4 2.0 - - - -
105A ALA* 3.5 24.5 - - + -
145A ILE* 4.2 12.6 - - + -
148A ASP* 4.1 22.2 - - + -
150A PHE* 3.5 50.7 - + + -
151A PHE* 4.9 0.2 - + - -
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Residues in contact with CYS 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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13A TYR* 3.7 27.8 - - + +
14A PHE* 1.3 76.5 - - - +
16A ARG* 1.3 69.1 + - - +
37A PHE* 3.9 14.4 - - - -
41A VAL* 4.1 16.2 - - + -
85A MET* 4.1 11.0 - - - -
104A VAL* 2.9 61.3 + - - +
106A ILE* 5.2 0.7 - - - -
150A PHE* 3.5 1.9 - - - -
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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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15A CYS* 1.3 81.5 - - - +
17A GLY* 1.3 59.8 + - - +
37A PHE* 4.1 2.9 - - - -
41A VAL* 3.7 13.2 - - - +
101A ILE* 3.9 13.2 - - + -
102A LEU 3.2 9.9 - - - +
103A ASN* 3.0 27.6 + - - +
150A PHE* 2.9 50.4 + - + +
153A VAL* 3.5 17.5 - - - +
154A SER* 3.0 23.0 + - - +
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Residues in contact with GLY 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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16A ARG* 1.3 76.0 - - - +
18A GLN* 1.3 65.8 + - - -
37A PHE* 3.3 20.3 - - - -
38A PRO* 4.5 0.7 - - - -
40A GLN* 5.9 1.3 - - - -
41A VAL* 4.0 10.5 - - - -
101A ILE* 3.5 9.0 - - - +
102A LEU* 2.9 30.7 + - - +
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Residues in contact with GLN 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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17A GLY* 1.3 71.3 - - - -
19A VAL* 1.3 62.9 + - - +
20A VAL* 3.5 7.0 + - + +
36A ASN 3.5 5.2 - - - +
37A PHE* 3.5 1.0 - - - -
38A PRO* 3.0 36.7 - - + +
99A GLY* 4.2 17.6 + - - +
100A GLU 3.5 6.3 - - - +
101A ILE* 3.2 22.9 - - + +
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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