Contacts of the strand formed by residues 114 - 121 (chain B) in PDB entry 4BEI
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 VAL 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.4 7.7 + - - +
62B LEU* 2.7 50.2 + - + +
64B ILE* 6.5 0.2 - - + -
76B TYR* 3.7 24.2 - - + +
112B LEU* 3.9 22.7 - - + -
113B ASN* 1.3 80.1 - - - +
115B THR* 1.3 77.0 + - - +
116B ARG* 3.8 16.4 - - + +
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Residues in contact with THR 115 (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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59B SER* 3.8 16.8 - - - +
60B SER 3.5 12.8 - - - +
61B GLN* 2.7 24.7 + - + +
114B VAL* 1.3 84.6 - - - +
116B ARG* 1.3 67.5 + - - +
117B GLY 5.1 0.9 - - - +
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Residues in contact with ARG 116 (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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60B SER* 2.6 55.6 + - - +
62B LEU* 4.2 10.1 - - + +
76B TYR* 4.0 26.1 + - - -
77B TRP* 4.5 6.7 - - - +
78B LEU* 3.8 44.0 + - + +
90B ALA* 5.3 3.6 - - - +
91B LYS* 4.6 27.1 - - - +
114B VAL* 3.8 12.9 + - + +
115B THR* 1.3 81.3 - - - +
117B GLY* 1.3 61.9 + - - +
118B PHE* 4.7 1.8 - - - -
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Residues in contact with GLY 117 (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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57B TYR* 3.2 26.0 + - - -
58B ILE 3.3 9.6 - - - -
59B SER* 4.0 4.0 - - - -
78B LEU* 6.1 0.2 - - - -
90B ALA* 4.8 4.2 - - - +
91B LYS* 5.9 0.7 - - - -
115B THR* 5.1 1.4 - - - +
116B ARG* 1.3 81.3 + - - +
118B PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 118 (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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219A ARG* 4.0 3.1 - - - +
46B LEU* 4.9 0.4 - - + -
57B TYR* 3.5 10.3 - - - -
58B ILE* 2.9 65.6 + - + -
60B SER* 4.6 7.9 - - - -
78B LEU* 4.4 10.1 - - + -
80B ILE* 3.8 21.1 - - + -
90B ALA* 3.6 38.6 - - + +
116B ARG 4.7 0.7 - - - -
117B GLY* 1.3 77.4 - - - +
119B TRP* 1.3 61.7 + - - +
120B VAL* 3.6 29.3 + - + -
131B VAL* 3.6 34.1 - - + -
149B PHE* 4.2 4.5 - + - -
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Residues in contact with TRP 119 (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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219A ARG* 2.4 39.9 + - - +
54B ASN 5.9 1.1 - - - -
55B GLY 5.1 0.4 - - - -
56B GLY* 3.4 36.1 - - - -
57B TYR* 3.8 32.6 - + + -
118B PHE* 1.3 76.2 - - - +
120B VAL* 1.3 66.1 + - - +
121B PRO* 4.5 12.6 - - + -
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Residues in contact with VAL 120 (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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219A ARG* 4.3 0.4 - - - +
51B LEU* 3.7 19.1 - - + -
55B GLY* 3.2 2.1 - - - -
56B GLY 2.9 32.1 + - - +
58B ILE* 4.4 1.8 - - + -
88B PHE* 4.6 8.5 - - + -
118B PHE* 3.6 27.4 - - + +
119B TRP* 1.3 77.7 - - - +
121B PRO* 1.3 66.2 - - - +
124B MET* 4.4 11.0 - - + -
129B TYR* 4.8 7.2 - - + -
149B PHE* 3.9 23.1 - - + -
151B LYS* 3.9 24.7 - - + -
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Residues in contact with PRO 121 (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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201A GLU* 3.9 8.3 - - - +
219A ARG* 3.5 18.6 - - - +
221A LYS* 5.6 3.6 - - - +
55B GLY* 4.2 0.7 - - - -
119B TRP* 3.7 14.6 - - + +
120B VAL* 1.3 92.9 - - - +
122B GLU* 1.3 65.6 + - - +
123B TYR* 3.3 44.2 - - + +
124B MET* 3.1 31.8 + - + +
151B LYS* 3.4 4.7 - - - -
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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