Contacts of the strand formed by residues 4 - 13 (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 SER 4 (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* 1.3 80.3 - - - +
5A ARG* 1.3 60.0 + - - +
6A LEU* 4.2 2.6 + - - +
71A VAL* 5.8 1.3 - - - -
79A GLU* 3.1 10.6 + - - +
80A LEU* 3.3 22.9 - - - -
82A ASP* 3.7 25.9 + - - +
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Residues in contact with ARG 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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4A SER* 1.3 74.1 - - - +
6A LEU* 1.3 87.4 + - - +
7A TYR* 3.3 33.3 - - + +
38A LYS* 3.3 33.7 - - + +
39A VAL 3.0 27.9 + - - +
40A GLN* 5.2 2.2 - - - +
79A GLU* 3.4 17.5 + - + +
80A LEU 2.8 12.6 + - - +
82A ASP* 2.8 25.8 + - - -
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Residues in contact with LEU 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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4A SER* 4.2 2.2 + - - +
5A ARG* 1.3 101.2 + - - +
7A TYR* 1.3 60.2 - - - +
38A LYS* 3.5 3.5 - - - -
39A VAL* 3.1 31.4 + - + -
45A ILE* 3.9 24.5 - - + -
82A ASP* 3.5 25.8 - - + +
84A HIS* 3.7 20.9 - - + +
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Residues in contact with TYR 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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5A ARG* 3.3 35.5 - - + +
6A LEU* 1.3 75.0 - - - +
8A THR* 1.3 66.6 + - - +
27A PHE* 6.5 0.7 - + - -
37A GLY* 3.2 23.1 - - - +
38A LYS* 3.2 39.5 - - + -
39A VAL* 4.1 2.4 - - - +
81A MET* 3.7 43.8 - - + +
82A ASP 3.0 7.3 + - - +
83A VAL* 4.0 16.2 - - + -
84A HIS* 2.9 27.2 + - - +
201A 2GD 3.7 23.6 - + + -
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Residues in contact with THR 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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7A TYR* 1.3 79.4 - - - +
9A LEU* 1.3 60.6 + - - +
35A PHE 5.0 0.3 + - - -
36A GLY* 3.0 21.8 - - - -
37A GLY 3.0 8.6 + - - -
39A VAL* 3.7 11.4 - - + -
45A ILE* 3.4 42.0 - - + +
48A GLY 3.9 0.3 + - - -
49A ALA* 3.5 29.9 + - + +
52A GLU* 3.5 19.2 - - - +
83A VAL* 4.3 2.5 - - - -
84A HIS 3.2 7.6 - - - -
86A PHE* 4.2 1.6 - - + -
201A 2GD 3.2 8.1 - - - +
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Residues in contact with LEU 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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8A THR* 1.3 77.0 - - - +
10A VAL* 1.3 64.0 + - - +
11A LEU* 4.3 9.2 - - + -
33A ASN* 3.8 26.7 - - - +
34A GLY* 3.6 32.5 - - - +
35A PHE 3.5 6.3 - - - +
36A GLY* 4.5 2.2 - - - +
70A ILE* 5.9 0.9 - - + -
72A PHE* 6.5 0.2 - - + -
83A VAL* 3.8 14.1 - - + -
84A HIS 3.0 7.0 + - - +
85A VAL* 3.3 12.9 - - + +
86A PHE* 2.9 25.6 + - - +
123A TRP* 3.9 30.5 - - + -
201A 2GD 3.9 20.4 - - + +
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Residues in contact with VAL 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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8A THR* 5.1 0.4 - - - +
9A LEU* 1.3 80.0 - - - +
11A LEU* 1.3 72.2 + - - +
34A GLY* 3.6 3.8 - - - -
35A PHE* 2.8 44.4 + - - +
49A ALA* 3.6 44.4 - - + +
53A LEU* 4.0 26.9 - - + -
64A LEU* 3.8 22.9 - - + -
86A PHE* 3.4 11.0 - - + +
88A THR* 4.3 3.6 - - + -
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Residues in contact with LEU 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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9A LEU* 4.3 8.7 - - + -
10A VAL* 1.3 77.4 - - - +
12A VAL* 1.3 63.2 + - - +
13A LEU* 3.5 1.8 + - + -
18A VAL* 4.5 6.3 - - + -
19A LEU 4.4 4.7 - - - +
20A LEU* 3.8 13.2 - - + -
34A GLY* 3.8 22.9 - - - +
85A VAL* 3.9 17.5 - - + -
86A PHE 2.9 9.8 + - - +
87A CYS* 3.2 6.2 - - - -
88A THR* 3.1 23.9 + - - +
123A TRP* 4.2 12.3 - - + -
124A PHE* 3.7 31.2 - - + -
127A LEU* 3.8 34.8 - - + -
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Residues in contact with VAL 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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10A VAL* 4.1 0.6 + - + -
11A LEU* 1.3 70.7 - - - +
13A LEU* 1.3 57.5 + - - +
14A GLN* 4.1 5.4 - - + -
18A VAL* 3.4 5.6 - - - +
19A LEU* 3.0 42.4 + - + -
35A PHE* 5.1 2.0 - - + -
53A LEU* 3.9 32.1 - - + -
59A LEU* 4.2 13.2 - - + -
88A THR* 3.4 22.7 - - + +
89A ASP* 5.4 0.4 - - - -
91A ILE* 4.1 21.5 - - + -
105A TRP* 3.8 24.9 - - + -
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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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11A LEU 3.5 1.3 + - - +
12A VAL* 1.3 72.7 - - - +
14A GLN* 1.3 75.5 + - - +
17A ARG 3.8 7.4 - - - +
18A VAL* 4.1 10.8 - - + -
87A CYS* 3.6 14.6 - - - -
88A THR 2.9 9.8 + - - +
89A ASP* 3.3 22.0 - - - +
108A LEU* 4.0 12.6 - - + -
127A LEU* 3.7 29.4 - - + +
128A LEU* 3.8 28.7 - - + +
130A LYS* 3.3 35.0 + - - +
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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