Contacts of the strand formed by residues 80 - 88 (chain A) in PDB entry 4N1T
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 LEU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ALA* 2.9 24.6 + - + +
4A SER* 3.9 12.6 - - - -
5A ARG* 2.8 26.5 + - - +
71A VAL* 4.0 20.0 - - + -
72A PHE 3.4 5.8 - - - +
73A GLU* 3.7 39.9 - - + +
74A PHE 5.3 0.2 - - - +
77A GLU 5.4 2.5 - - - +
78A PRO 4.5 5.6 - - - +
79A GLU* 1.3 79.2 - - - +
81A MET* 1.3 60.9 + - - +
136A TYR* 5.5 2.9 - - + -
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Residues in contact with MET 81 (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 ARG 3.8 4.0 - - - -
7A TYR* 3.7 42.2 - - + +
27A PHE* 4.4 11.9 - - + -
70A ILE 3.6 1.7 - - - +
71A VAL* 3.2 7.8 - - - +
72A PHE* 2.9 48.2 + - + +
74A PHE* 3.8 28.9 - - + -
79A GLU 5.2 2.5 - - - +
80A LEU* 1.3 75.2 - - - +
82A ASP* 1.3 60.0 + - - +
83A VAL* 3.7 11.2 - - + +
201A 2GD 3.8 39.5 - - + -
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Residues in contact with ASP 82 (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 SER* 3.7 23.3 + - - +
5A ARG 2.8 17.7 + - - +
6A LEU* 3.5 13.1 - - + +
7A TYR* 3.0 24.9 + - - +
69A GLN* 2.7 38.3 + - - +
70A ILE 4.0 1.6 - - - -
71A VAL* 4.3 11.1 - - + +
80A LEU 3.8 0.4 + - - -
81A MET* 1.3 70.9 - - - +
83A VAL* 1.3 61.0 + - - +
84A HIS* 3.5 16.0 + - - -
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Residues in contact with VAL 83 (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 TYR* 3.5 14.4 - - + +
8A THR 4.3 3.4 - - - -
9A LEU* 3.8 25.1 - - + +
69A GLN* 3.2 6.9 - - - +
70A ILE* 2.8 43.7 + - + +
72A PHE* 3.7 35.0 - - + -
81A MET* 4.1 11.2 - - + -
82A ASP* 1.3 73.5 + - - +
84A HIS* 1.3 63.4 + - - +
85A VAL* 3.8 9.1 + - + +
201A 2GD 3.5 26.0 - - + -
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Residues in contact with HIS 84 (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 LEU* 3.7 17.0 - - + +
7A TYR 2.9 11.7 + - - +
8A THR* 3.2 4.0 - - - -
9A LEU 3.0 22.3 + - - -
45A ILE* 3.6 41.0 - - + +
66A LYS* 6.3 2.7 - - - -
68A GLY 3.7 4.9 - - - +
69A GLN* 3.6 21.0 + - + +
82A ASP* 3.5 40.2 + - - -
83A VAL* 1.3 71.8 - - - +
85A VAL* 1.3 59.0 + - - +
86A PHE* 3.5 15.6 - + + -
156A VAL* 5.7 5.2 - - + -
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Residues in contact with VAL 85 (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 LEU* 3.3 16.6 - - + +
11A LEU* 3.9 21.1 - - + -
66A LYS* 3.8 2.4 - - - +
67A VAL* 2.9 37.3 + - + -
68A GLY* 2.8 29.5 + - - +
70A ILE* 4.1 24.5 - - + -
83A VAL* 4.1 18.6 - - + +
84A HIS* 1.3 75.4 - - - +
86A PHE* 1.3 65.9 + - - +
123A TRP* 4.4 7.0 - - + -
127A LEU* 4.1 6.1 - - + -
133A PHE* 4.5 4.0 - - + -
156A VAL* 5.4 0.2 - - - +
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 4.2 0.9 - - + -
9A LEU 2.9 10.4 + - - +
10A VAL* 3.4 5.1 - - + -
11A LEU* 2.9 29.0 + - - +
45A ILE* 4.0 20.4 - - + -
46A GLU* 3.9 29.6 - - + -
49A ALA* 3.6 23.8 - - + -
64A LEU* 4.1 26.9 - - + -
65A HIS 3.1 22.4 - - - +
66A LYS* 3.7 27.4 - - + -
67A VAL* 4.0 3.3 - - - +
84A HIS* 3.5 35.2 - + + -
85A VAL* 1.3 74.1 - - - +
87A CYS* 1.3 63.3 + - - +
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Residues in contact with CYS 87 (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 LEU 3.2 13.9 - - - +
13A LEU* 3.6 29.4 - - - -
64A LEU* 3.8 2.1 - - - -
65A HIS* 2.9 36.9 + - + +
67A VAL* 3.7 24.7 - - + -
86A PHE* 1.3 77.0 - - - +
88A THR* 1.3 65.8 + - - +
127A LEU* 4.2 12.1 - - + -
130A LYS* 3.7 19.3 - - - +
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Residues in contact with THR 88 (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 VAL* 4.3 4.9 - - + -
11A LEU 3.1 5.2 + - - +
12A VAL* 3.4 18.2 - - + +
13A LEU 2.9 26.5 + - - +
53A LEU* 4.4 1.1 - - + -
61A VAL* 3.3 17.3 - - + +
63A ALA 2.8 24.6 + - - -
64A LEU* 4.0 8.1 - - + -
65A HIS* 4.7 0.7 - - - -
87A CYS* 1.3 78.2 - - - +
89A ASP* 1.3 57.7 + - - +
90A SER* 3.0 22.5 + - - -
91A ILE* 3.9 15.5 - - + -
204A SO4 3.2 5.6 + - - -
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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