Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 4CEV
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 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 3.8 29.6 - - + -
109B VAL* 4.0 12.1 - - + -
110B ALA* 3.8 32.3 - - + +
113B TYR* 3.9 33.3 + - + +
114B GLU 4.1 0.2 - - - -
115B ARG* 1.3 73.5 - - - +
117B GLY* 1.3 67.5 + - - +
163B LYS 4.9 2.3 + - - +
164B ILE* 3.6 25.5 - - + +
168B HIS* 3.7 12.1 + - - +
218B THR* 4.3 0.9 - - - -
219B ASP* 3.7 0.6 + - - -
220B GLY* 3.4 25.8 - - - +
221B VAL 3.9 2.2 - - - +
222B HIS* 4.1 7.9 - - + +
265B THR* 4.3 3.1 - - - +
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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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115B ARG 3.5 2.0 + - - -
116B LEU* 1.3 74.5 - - - +
118B VAL* 1.3 68.2 + - - +
168B HIS 3.1 13.9 - - - -
214B LEU* 4.3 1.3 - - - -
218B THR* 3.6 16.5 - - - +
220B GLY 2.8 13.1 + - - -
221B VAL* 3.3 9.3 - - - -
222B HIS 2.9 24.3 + - - -
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Residues in contact with VAL 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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106B LEU* 4.0 15.0 - - + -
117B GLY* 1.3 81.5 - - - +
119B ILE* 1.3 69.8 + - - +
120B TRP* 3.8 33.8 + - + +
143B LEU* 4.8 4.3 - - + -
164B ILE* 3.6 36.3 - - + -
168B HIS 2.8 9.7 + - - +
169B VAL* 3.4 12.7 - - + +
170B VAL* 2.9 27.9 + - - +
214B LEU* 4.4 2.4 - - - +
221B VAL* 4.5 0.4 - - - +
222B HIS* 3.4 17.7 - - + +
224B SER* 4.7 0.2 - - - -
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Residues in contact with ILE 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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118B VAL* 1.3 73.2 - - - +
120B TRP* 1.3 59.3 + - - +
121B TYR* 3.6 9.8 + - + +
170B VAL 3.4 4.7 - - - +
172B ILE* 3.8 25.8 - - + -
207B MET* 5.1 1.3 - - + -
210B THR* 3.9 17.7 - - + -
214B LEU* 3.5 22.7 - - + -
221B VAL* 4.0 16.8 - - + +
222B HIS 3.0 8.1 + - - +
223B LEU* 3.8 19.1 - - + +
224B SER* 2.9 28.6 + - - +
258B LEU* 3.6 34.1 - - + -
263B ILE* 4.6 2.9 - - + -
264B ILE* 4.1 4.7 - - + -
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Residues in contact with TRP 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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99B HIS* 3.2 21.8 - + - -
102B ALA* 3.5 28.3 - - + -
106B LEU* 4.3 13.2 - - + -
118B VAL* 3.8 16.3 + - + -
119B ILE* 1.3 71.7 - - - +
121B TYR* 1.3 60.7 + - - +
122B ASP* 3.2 27.6 + - + -
124B HIS 4.0 1.8 - - - -
125B GLY 4.2 0.7 - - - -
126B ASP* 3.0 34.2 + - + +
142B PRO* 3.7 9.4 - - + -
143B LEU* 3.8 39.9 - - + -
169B VAL* 5.0 1.3 - - + -
170B VAL 2.9 12.0 + - - +
171B LEU* 3.5 33.7 - - + +
172B ILE 2.9 24.1 + - - +
224B SER* 3.6 25.6 - - - -
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Residues in contact with TYR 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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119B ILE* 3.6 5.8 + - + -
120B TRP* 1.3 68.2 - - - +
122B ASP* 1.3 62.1 + - - +
172B ILE* 3.5 26.2 - - + -
203B MET* 3.5 13.4 - - + +
207B MET* 5.3 0.9 - - - -
223B LEU* 4.6 5.8 - - + -
224B SER 3.1 10.7 + - - +
225B LEU* 3.7 40.2 - - + -
226B ASP* 2.8 37.8 + - - +
229B GLY* 4.8 2.9 - - - -
230B LEU* 4.2 9.6 - - + -
246B LEU* 3.4 30.7 - - + +
251B SER* 2.9 42.2 + - - -
254B ALA* 4.0 19.3 - - + -
255B MET* 4.5 7.4 - - + -
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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