Contacts of the strand formed by residues 89 - 101 (chain B) in PDB entry 1N2Q
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 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B LEU* 3.7 1.4 - - - -
85B THR* 2.6 46.9 + - - +
86B PHE 3.9 10.1 - - - +
87B GLY* 3.0 4.6 - - - +
88B GLN* 1.3 76.3 - - - +
90B GLU* 1.3 74.0 + - - +
91B GLN* 3.7 22.4 - - + +
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 4.5 7.6 - - + +
46B LYS* 2.6 39.4 + - - +
82B ASN* 3.7 31.3 + - + +
83B ILE 3.7 6.1 - - - +
84B LEU* 4.6 12.2 - - + +
88B GLN 3.5 3.7 + - - +
89B LEU* 1.3 84.0 - - - +
91B GLN* 1.3 62.1 + - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.3 35.6 - - - -
82B ASN* 3.1 11.1 - - - +
83B ILE* 2.9 44.8 + - + -
85B THR* 2.9 36.1 + - - +
89B LEU* 3.7 19.6 - - + +
90B GLU* 1.3 79.1 - - - +
92B ASN* 1.3 60.9 + - - +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B CYS* 5.2 2.9 - - - +
80B THR* 3.7 16.4 - - - +
81B CYS 3.2 6.4 - - - +
82B ASN* 3.3 10.9 - - - +
83B ILE* 3.7 7.3 - - - +
91B GLN* 1.3 77.2 - - - +
93B VAL* 1.3 71.6 + - - +
94B TYR* 3.2 10.9 + - - +
141F ASP* 2.9 32.1 + - - +
143F THR* 3.0 21.4 + - - +
144F THR* 3.1 23.7 - - + +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 3.9 1.4 - - - +
6B CYS* 4.8 3.6 - - + -
7B GLY* 3.4 36.2 + - - +
8B TYR 4.2 0.4 - - - +
26B CYS* 3.7 20.4 - - - -
28B LEU* 3.7 16.2 - - + -
81B CYS* 2.8 28.9 + - - +
82B ASN* 3.8 1.3 - - - -
83B ILE* 3.4 42.0 - - + -
92B ASN* 1.3 80.7 + - - +
94B TYR* 1.3 61.5 + - + +
144F THR* 3.4 20.4 + - - +
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 4.1 13.2 - - + -
7B GLY 3.6 14.1 - - - -
8B TYR* 3.6 27.1 - - + -
9B ILE* 3.4 27.9 - - + +
12B GLU* 3.0 38.9 + - + -
80B THR* 3.6 0.7 - - - -
81B CYS 2.8 25.6 + - - +
92B ASN* 3.2 12.2 + - - +
93B VAL* 1.3 83.7 - - + +
95B GLY* 1.3 82.7 + - - +
96B ILE* 3.8 11.7 - - + -
139F THR 3.8 1.6 - - - -
140F PRO* 3.1 39.9 - - + +
141F ASP* 4.0 7.4 - - - -
144F THR* 4.7 2.2 - - - -
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.4 0.2 - - - -
78B GLN* 5.3 1.1 - - - -
79B LEU 3.4 12.8 - - - -
80B THR* 4.1 6.3 - - - -
94B TYR* 1.3 85.9 - - - +
96B ILE* 1.3 67.4 + - - +
138F THR* 3.7 13.8 - - - +
139F THR 4.1 4.0 - - - +
141F ASP* 4.4 15.4 + - - +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.6 36.3 - - + +
11B PRO 3.7 14.4 - - - +
12B GLU* 3.1 20.9 - - - +
14B PRO* 4.7 5.6 - - + -
22B PHE* 5.0 2.5 - - + -
24B ALA* 4.7 4.0 - - + -
78B GLN* 3.8 3.5 + - - +
79B LEU* 2.9 58.0 + - + +
94B TYR* 3.8 22.4 - - + -
95B GLY* 1.3 79.9 - - - +
97B THR* 1.3 63.8 + - - +
98B ILE* 4.3 13.2 - - + -
138F THR* 3.5 5.8 - - - +
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 3.7 17.1 + - - -
14B PRO* 3.8 8.4 - - - +
76B ASN* 3.3 26.2 - - - +
77B ILE 3.9 3.6 - - - +
78B GLN* 4.8 9.0 - - + +
96B ILE* 1.3 75.5 + - - +
98B ILE* 1.3 63.2 + - - +
99B ILE* 3.8 21.0 + - + +
138F THR* 3.0 26.6 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 3.7 33.2 - - + +
22B PHE* 3.8 20.9 - - + -
69B PHE* 4.1 7.6 - - + -
72B ILE* 4.2 23.3 - - + -
74B SER 5.2 0.2 - - - +
75B LEU 4.3 0.2 - - - -
76B ASN* 3.3 6.6 - - - +
77B ILE* 2.8 65.3 + - + +
79B LEU* 3.6 28.5 - - + -
96B ILE* 4.3 9.0 - - + -
97B THR* 1.3 73.0 - - - +
99B ILE* 1.3 67.7 + - - +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 6.3 0.9 - - - -
14B PRO 3.1 6.1 + - - +
15B VAL* 3.0 27.8 - - + +
16B VAL* 3.0 24.4 + - - +
75B LEU* 3.3 14.1 - - + +
76B ASN* 4.9 2.9 - - + +
97B THR* 3.8 23.6 + - + +
98B ILE* 1.3 80.0 - - - +
100B SER* 1.3 68.4 + - - +
131B HIS 5.5 2.2 - - - +
132B LEU* 4.3 23.6 - - + -
135F ASP 4.9 5.6 - - - +
136F ALA* 5.4 7.0 - - + -
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.0 14.6 - - - -
18B LEU* 3.3 25.5 - - - +
72B ILE* 3.9 20.0 - - - +
74B SER 2.8 28.0 + - - -
75B LEU* 3.1 23.6 + - - +
99B ILE* 1.3 83.4 - - - +
101B GLY* 1.3 59.0 + - - +
131B HIS* 4.5 3.1 - - - +
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 4.5 4.0 - - - +
16B VAL 2.9 7.3 + - - -
17B GLN* 3.2 3.3 - - - -
18B LEU* 2.8 33.4 + - - +
99B ILE 4.3 0.2 - - - -
100B SER* 1.3 74.4 - - - +
102B LEU* 1.3 65.8 + - - +
130B THR 3.3 13.2 - - - -
131B HIS* 4.2 6.5 - - - -
132B LEU* 4.2 10.5 - - - -
182B LEU* 3.6 6.5 - - - +
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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