Contacts of the strand formed by residues 81 - 91 (chain A) in PDB entry 1N2F
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 4.4 3.6 - - - -
65A MET* 5.6 0.7 - - - +
79A ASP 3.7 3.7 + - - -
80A ALA* 1.3 77.7 - - - +
82A ILE* 1.3 69.3 + - - +
83A THR* 5.3 1.9 + - - -
102A HIS 3.9 0.8 - - - +
103A ILE* 4.4 0.9 - - - +
104A ASN* 3.0 48.2 + - - +
13B THR* 4.4 11.3 - - - +
14B ALA 3.4 14.4 - - - -
15B THR* 3.9 12.3 - - - -
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Residues in contact with ILE 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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58A SER* 3.6 32.1 - - - +
61A PHE* 3.7 24.2 - - + -
62A ILE* 3.4 27.1 - - + +
65A MET* 3.7 19.5 - - + -
81A SER* 1.3 82.8 - - - +
83A THR* 1.3 63.2 + - - +
84A GLY 3.6 0.3 + - - -
101A LEU* 3.9 28.7 - - + -
102A HIS 3.4 6.1 - - - +
103A ILE* 4.0 12.3 - - + -
12B ALA 3.6 2.3 - - - +
13B THR* 3.3 2.7 - - - -
14B ALA 2.9 29.9 + - - -
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Residues in contact with THR 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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81A SER* 5.3 2.1 + - - -
82A ILE* 1.3 70.2 - - - +
84A GLY* 1.3 58.7 + - - +
85A LYS* 4.3 13.5 - - - +
100A GLU 3.7 0.2 - - - +
102A HIS* 3.0 48.9 + - + +
11B THR* 3.5 29.6 - - + -
12B ALA 3.4 3.6 - - - -
13B THR* 3.2 24.3 + - - +
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Residues in contact with GLY 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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54A ALA* 3.8 9.8 - - - +
58A SER* 3.3 21.9 + - - -
83A THR* 1.3 74.5 - - - +
85A LYS* 1.3 61.9 + - - +
86A VAL* 4.2 0.9 - - - -
100A GLU 3.6 6.1 - - - -
101A LEU* 3.7 11.9 - - - -
11B THR* 3.3 3.6 - - - +
12B ALA 2.8 37.1 + - - +
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Residues in contact with LYS 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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83A THR* 4.3 7.0 - - - +
84A GLY* 1.3 75.7 - - - +
86A VAL* 1.3 64.0 + - - +
87A GLY 4.0 0.4 + - - -
98A GLU 3.8 0.5 - - - +
99A VAL* 3.4 5.9 - - - +
100A GLU* 3.0 41.4 + - + +
101A LEU* 4.9 0.4 - - - +
102A HIS* 3.4 36.8 - - + +
9B THR* 3.9 14.4 - - + -
10B ALA 3.1 6.7 - - - +
11B THR* 3.4 34.8 + - + +
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Residues in contact with VAL 86 (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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50A GLU* 3.6 33.4 - - + +
53A PHE* 3.8 25.6 - - + -
54A ALA* 3.6 32.5 - - - +
57A TYR* 5.6 1.3 - - + -
84A GLY 5.2 0.2 - - - -
85A LYS* 1.3 77.0 - - - +
87A GLY* 1.3 70.3 + - - +
97A LEU* 4.2 10.1 - - + -
98A GLU 3.5 7.0 - - - +
99A VAL* 4.1 15.3 - - + -
8B TYR 3.9 0.3 - - - +
9B THR* 3.4 1.9 - - - -
10B ALA 2.8 33.8 + - - +
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Residues in contact with GLY 87 (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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85A LYS 4.0 1.2 - - - -
86A VAL* 1.3 76.5 - - - +
88A ILE* 1.3 60.6 + - - -
97A LEU* 3.3 10.3 - - - +
98A GLU* 2.9 39.9 + - - +
4B ILE* 3.8 5.6 - - - -
6B ALA* 4.0 7.0 - - - -
8B TYR 3.2 9.2 - - - -
9B THR* 3.7 13.5 - - - +
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Residues in contact with ILE 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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18A ARG* 3.4 32.1 - - - +
39A MET* 3.8 35.2 - - + -
50A GLU* 3.6 23.6 - - + +
87A GLY* 1.3 75.5 - - - +
89A GLY* 1.3 62.1 + - - +
95A PHE* 4.2 14.8 - - + -
96A GLY 3.4 11.0 - - - +
97A LEU* 4.0 3.4 - - + -
4B ILE* 3.7 2.9 - - - -
6B ALA* 4.1 0.4 - - - +
7B LEU* 2.7 24.5 + - - +
8B TYR* 2.9 17.7 + - + +
125B PRO* 3.9 15.7 - - + -
172B DTT 4.6 4.5 - - + -
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Residues in contact with GLY 89 (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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88A ILE* 1.3 76.7 - - - +
90A GLN* 1.3 61.2 - - - -
95A PHE* 3.2 13.2 - - - +
96A GLY 2.8 34.7 + - - -
4B ILE* 3.3 9.5 - - - +
5B LYS 3.7 17.7 - - - -
7B LEU* 4.1 7.6 - - - -
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Residues in contact with GLN 90 (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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89A GLY* 1.3 71.9 - - - -
91A ILE* 1.3 98.7 + - - +
92A PRO* 3.7 7.5 - - - +
94A GLY 3.8 7.2 - - - +
95A PHE* 4.3 10.9 - - + -
2B GLN* 5.2 0.2 + - - -
3B THR 4.9 0.7 - - - +
4B ILE* 3.9 9.5 - - - +
5B LYS 4.4 5.2 + - - -
7B LEU* 4.5 10.7 - - + +
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Residues in contact with ILE 91 (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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90A GLN* 1.3 94.2 + - - +
92A PRO* 1.3 84.8 - - + +
93A GLY 2.9 4.0 + - - -
94A GLY* 3.0 20.6 + - - +
95A PHE 3.1 30.1 - - - +
96A GLY* 3.5 9.9 - - - +
2B GLN* 3.6 27.1 - - + +
4B ILE* 3.4 24.7 - - + -
122B GLN 5.3 0.7 - - - +
128B ASN* 3.4 23.8 - - + +
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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