Contacts of the strand formed by residues 87 - 98 (chain B) in PDB entry 2E7A
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 HIS 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B ARG 5.8 0.4 - - - -
83B ILE* 4.3 1.6 - - - +
84B SER* 3.1 32.2 + - - +
85B THR 3.5 0.6 - - - -
86B THR* 1.3 86.1 + - - +
88B ASN* 1.3 64.3 + - - +
89B GLN* 3.0 51.3 + - + +
90B PRO 5.0 0.2 + - - -
91B VAL* 3.7 22.4 - - + +
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Residues in contact with ASN 88 (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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83B ILE* 4.3 12.9 - - - +
84B SER 4.7 3.9 - - - +
85B THR 5.2 5.4 - - - +
86B THR 5.8 0.9 - - - -
87B HIS* 1.3 75.4 + - - +
89B GLN* 1.3 71.1 + - + +
90B PRO* 3.4 10.4 - - - +
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Residues in contact with GLN 89 (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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82B ARG 4.4 1.2 - - - +
83B ILE* 5.1 0.2 - - - -
87B HIS* 3.0 51.2 + - + +
88B ASN* 1.3 84.4 + - + +
90B PRO* 1.3 76.1 - - + +
91B VAL* 3.7 0.5 + - - +
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Residues in contact with PRO 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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81B SER* 4.5 14.6 - - - +
82B ARG 3.4 9.0 - - - +
83B ILE* 3.6 31.4 - - + -
87B HIS* 5.0 0.3 + - - -
88B ASN 3.4 5.6 - - - +
89B GLN* 1.3 95.8 - - + +
91B VAL* 1.3 62.8 + - - +
92B ASN* 4.4 2.1 + - - +
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Residues in contact with VAL 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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34A ASN* 3.8 25.8 - - - +
147A SER* 5.8 4.0 - - - -
81B SER* 3.2 2.2 - - - -
82B ARG* 2.8 40.8 + - + +
87B HIS* 3.7 29.8 - - + +
89B GLN 3.9 0.2 - - - +
90B PRO* 1.3 78.4 - - - +
92B ASN* 1.3 75.9 + - - +
93B LEU* 3.3 2.2 + - + +
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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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146A GLU* 5.5 7.9 - - - +
147A SER* 4.0 34.4 + - - +
148A GLY* 4.3 1.9 + - - -
79B THR* 4.4 23.4 + - - +
80B ILE 3.8 4.7 - - - +
81B SER* 3.6 16.5 - - - +
90B PRO* 5.4 2.1 - - - +
91B VAL* 1.3 81.3 - - - +
93B LEU* 1.3 62.0 + - - +
95B SER* 4.6 12.5 + - - -
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Residues in contact with LEU 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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15A HIS* 4.9 2.8 + - - -
34A ASN* 3.6 37.7 - - + +
148A GLY* 3.5 13.5 - - - -
151A TYR* 5.0 0.7 - - - -
58B ILE* 3.7 24.7 - - + -
80B ILE* 2.9 11.0 + - + +
82B ARG* 3.8 37.2 - - + +
91B VAL* 4.1 2.5 - - + +
92B ASN* 1.3 76.5 - - - +
94B LEU* 1.3 73.8 + - + +
124B PHE* 3.6 35.4 - - + -
126B LEU* 4.5 4.3 - - + -
132B LEU* 4.0 11.9 - - + -
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Residues in contact with LEU 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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148A GLY 3.6 4.7 - - - -
151A TYR* 3.4 35.0 - - + +
58B ILE* 3.7 30.3 - - + -
79B THR* 3.2 1.9 - - - -
80B ILE* 2.8 51.2 + - + +
92B ASN* 3.5 0.8 - - - +
93B LEU* 1.3 90.1 + - + +
95B SER* 1.3 64.1 + - - +
120B LEU* 3.8 15.7 - - + +
121B GLY* 3.7 26.5 - - - +
122B GLY* 4.2 0.7 - - - +
124B PHE* 3.6 20.4 - - + -
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Residues in contact with SER 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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61A GLN* 2.9 18.4 + - - -
146A GLU* 6.0 0.5 - - - +
147A SER 3.9 19.3 - - - -
148A GLY 2.9 11.7 + - - +
149A GLN* 3.4 19.0 + - - +
77B THR* 5.8 0.2 - - - -
78B HIS 3.5 5.6 - - - -
79B THR* 3.5 21.5 - - - +
92B ASN* 4.6 9.3 + - - -
94B LEU* 1.3 77.6 - - - +
96B ALA* 1.3 66.4 + - - +
97B ILE* 4.9 3.8 - - - +
120B LEU* 3.8 5.4 - - - +
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Residues in contact with ALA 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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61A GLN* 4.0 5.6 - - - +
63A LEU* 4.9 5.4 - - - -
117A PRO* 4.0 22.0 - - + -
77B THR* 3.5 3.1 - - - -
78B HIS 3.0 30.4 + - - +
95B SER* 1.3 76.1 + - - +
97B ILE* 1.3 69.0 + - - +
118B ILE* 3.7 29.8 - - + +
119B TYR 5.2 0.9 - - - +
120B LEU* 3.8 9.4 - - + +
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Residues in contact with ILE 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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63A LEU* 3.6 10.4 - - + +
115A TYR* 3.3 63.8 - - + +
117A PRO* 3.4 18.3 - - - +
149A GLN* 3.9 19.5 - - - +
75B LEU* 4.2 20.4 - - + -
76B LEU 3.3 9.2 - - - +
77B THR* 4.1 14.6 - - + -
95B SER* 4.9 4.7 - - - +
96B ALA* 1.3 82.5 - - - +
98B ARG* 1.3 64.9 + - - +
118B ILE* 4.7 1.3 - - - -
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Residues in contact with ARG 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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98A ARG* 3.8 9.7 - - - +
100A PRO* 5.6 2.8 + - - +
114A TRP* 5.3 1.0 - - - +
115A TYR* 2.8 34.9 + - - -
116A GLU* 3.2 26.2 + - - +
117A PRO* 4.1 14.4 - - + -
75B LEU* 3.6 2.4 - - - -
76B LEU* 2.8 39.5 + - + +
97B ILE* 1.3 76.6 - - - +
99B SER* 1.3 88.2 + - - +
100B PRO* 3.3 4.4 - - - +
116B GLU* 2.7 49.9 + - + +
117B PRO 5.5 2.5 - - - +
118B ILE* 4.0 21.3 - - + -
98C ARG* 3.3 19.4 - - - +
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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