Contacts of the strand formed by residues 76 - 84 (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 LEU 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 3.6 54.5 - - + -
74B VAL* 4.6 1.6 - - + -
75B LEU* 1.3 73.9 - - - +
77B THR* 1.3 61.7 + - - +
97B ILE* 3.3 4.5 - - - -
98B ARG* 2.8 43.5 + - + +
100B PRO* 3.2 31.9 - - + -
114B TRP* 3.9 9.0 - - + -
116B GLU* 4.1 10.8 - - + -
118B ILE* 4.0 3.2 - - - +
137B ASN* 3.6 1.8 - - - -
138B ARG* 4.1 10.8 - - + -
141B TYR* 3.8 29.2 - - + -
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.7 4.0 - - - -
75B LEU* 4.7 4.3 - - + +
76B LEU* 1.3 80.6 - - - +
78B HIS* 1.3 62.4 + - - +
79B THR* 4.8 10.8 - - - +
96B ALA 3.5 6.1 - - - -
97B ILE* 4.1 24.7 - - + -
118B ILE* 4.6 0.9 - - - -
135B GLU 4.5 0.4 + - - -
136B ILE* 3.2 25.7 - - - +
137B ASN* 2.8 40.8 + - + +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TRP* 5.3 0.7 - + - -
60B SER* 3.0 39.7 + - - -
62B VAL* 3.4 42.8 - - + +
77B THR* 1.3 78.1 - - - +
79B THR* 1.3 72.8 + - - +
80B ILE* 5.1 0.2 - - + -
95B SER* 3.5 1.0 - - - -
96B ALA 3.0 29.8 + - - -
118B ILE* 3.7 35.2 - - + -
120B LEU* 3.5 21.8 - - + +
134B ALA* 4.3 15.0 - - + -
135B GLU 3.4 11.2 + - - -
136B ILE* 4.0 1.8 - - + +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 4.8 10.1 - - - +
78B HIS* 1.3 88.7 + - - +
80B ILE* 1.3 64.2 + - - +
81B SER* 4.8 1.6 + - - -
92B ASN* 4.4 22.2 + - - +
94B LEU 3.2 8.5 - - - -
95B SER* 3.5 19.7 - - - +
120B LEU* 3.9 2.5 - - - -
133B SER 3.5 1.4 - - - +
134B ALA* 3.4 2.9 - - - -
135B GLU* 3.0 48.8 + - - +
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Residues in contact with ILE 80 (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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58B ILE* 3.8 22.9 - - + -
59B TYR* 3.8 19.1 - - - +
60B SER* 3.7 26.2 - - - +
78B HIS* 5.1 0.2 - - + -
79B THR* 1.3 78.1 - - - +
81B SER* 1.3 67.3 + - - +
92B ASN* 3.7 1.6 - - - -
93B LEU* 2.9 27.4 + - + -
94B LEU* 2.8 37.1 + - + +
120B LEU* 4.0 8.9 - - + +
132B LEU* 4.8 5.4 - - + -
133B SER 3.1 10.5 - - - +
134B ALA* 4.1 12.1 - - + -
152B PHE* 4.1 14.8 - - + -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 4.0 4.6 + - - -
80B ILE* 1.3 78.7 - - - +
82B ARG* 1.3 60.3 + - - +
83B ILE* 5.4 2.3 - - - +
90B PRO* 4.5 16.7 - - - +
91B VAL 3.2 14.1 - - - -
92B ASN* 3.6 16.8 - - - -
93B LEU* 4.6 0.7 - - - -
131B ARG 3.7 0.5 - - - +
132B LEU* 3.4 8.5 - - - +
133B SER* 2.9 46.0 + - - -
135B GLU* 4.2 9.8 + - - -
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Residues in contact with ARG 82 (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* 2.9 30.6 + - - +
81B SER* 1.3 74.4 - - - +
83B ILE* 1.3 64.2 + - - +
84B SER* 3.3 22.0 + - - +
87B HIS* 5.8 0.2 - - - -
89B GLN 4.4 1.6 - - - +
90B PRO* 3.4 3.5 - - - +
91B VAL* 2.8 38.4 + - + +
93B LEU* 3.8 21.1 - - + +
125B GLN 4.1 15.0 + - - -
126B LEU* 3.7 13.1 - - - +
127B GLU* 3.7 21.6 - - - +
130B ASP* 2.8 33.5 + - - +
131B ARG 3.6 3.6 - - - +
132B LEU* 4.1 11.9 - - + -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 4.1 17.7 - - - +
81B SER* 5.4 3.8 - - - +
82B ARG* 1.3 75.2 - - - +
84B SER* 1.3 70.6 + - - +
87B HIS 4.3 8.5 - - - +
88B ASN* 4.3 9.2 - - - +
90B PRO* 3.6 36.6 - - + -
129B GLY 4.3 1.2 - - - +
130B ASP* 3.6 1.6 - - - -
131B ARG* 2.8 79.2 + - + +
133B SER* 6.0 3.8 - - - -
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Residues in contact with SER 84 (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* 3.3 29.3 + - - -
83B ILE* 1.3 82.9 - - - +
85B THR* 1.3 63.3 + - - +
86B THR* 3.1 16.4 - - - -
87B HIS* 3.1 34.2 + - - +
88B ASN* 4.3 2.1 + - - +
89B GLN 5.7 0.2 + - - -
130B ASP* 3.2 20.1 + - - +
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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