Contacts of the strand formed by residues 91 - 96 (chain F) in PDB entry 1CEV
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 PHE 91 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F LYS* 4.1 19.5 - - + +
3F PRO 2.7 17.0 + - - +
4F ILE* 3.3 12.4 - - + +
5F SER 2.9 24.1 + - - -
85F VAL* 4.1 0.7 - - - -
90F ARG* 1.3 70.3 - - - +
92F PRO* 1.3 81.2 - - + +
93F LEU* 4.1 3.6 - - + -
264F ILE* 3.5 20.9 - - + -
265F THR* 3.4 29.2 - - - -
266F SER* 3.4 17.9 - - - -
267F ALA* 3.6 13.0 - - + -
293F LEU* 5.1 0.7 - - + -
294F PHE* 3.4 41.3 - + - -
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Residues in contact with PRO 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F SER 3.7 5.4 - - - +
7F ILE* 5.2 1.8 - - + -
82F VAL* 4.2 20.9 - - + -
85F VAL* 3.9 16.8 - - + -
86F VAL* 4.1 20.4 - - + -
90F ARG 3.4 10.1 - - - +
91F PHE* 1.3 86.0 - - - +
93F LEU* 1.3 59.7 + - - +
94F VAL* 3.9 5.3 - - + +
105F THR* 5.7 0.7 - - + -
109F VAL* 4.1 7.0 - - + -
265F THR 3.9 13.9 - - - +
266F SER* 3.6 17.0 - - - -
267F ALA 3.3 22.3 + - - +
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Residues in contact with LEU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 3.8 17.0 - - + -
5F SER 2.9 9.5 + - - +
6F ILE* 3.2 21.0 - - + +
7F ILE* 3.0 22.3 + - - +
36F LEU* 3.7 29.6 - - + -
91F PHE* 3.5 3.5 + - + -
92F PRO* 1.3 71.4 - - - +
94F VAL* 1.3 61.1 + - - +
95F LEU* 3.9 6.6 + - + -
267F ALA* 3.5 16.6 - - + +
269F PHE* 4.2 15.3 - - + -
290F MET* 4.0 25.6 - - - -
294F PHE* 3.9 24.2 - - + -
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ILE* 3.2 17.0 - - + +
9F VAL* 3.6 25.1 - - + -
78F LEU* 4.1 5.6 - - + -
82F VAL* 4.0 18.6 - - + -
92F PRO 4.8 2.9 - - - -
93F LEU* 1.3 77.9 - - - +
95F LEU* 1.3 64.1 + - - +
101F ILE* 3.9 15.5 - - + -
105F THR* 3.7 36.1 - - + +
267F ALA 3.0 7.5 + - - +
268F GLU* 3.0 31.2 - - + +
269F PHE 3.1 6.6 + - - -
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 3.8 26.7 - - + -
7F ILE 2.8 9.7 + - - +
8F GLY* 3.4 3.1 - - - -
9F VAL* 2.9 24.9 + - - -
24F PRO* 3.7 20.8 - - + +
27F MET* 4.1 31.2 - - + -
28F ARG* 4.5 8.3 - - + +
32F VAL* 4.3 14.8 - - + -
93F LEU* 4.4 10.5 - - + -
94F VAL* 1.3 82.3 - - - +
96F GLY* 1.3 58.7 + - - +
101F ILE* 4.3 2.2 - - - -
269F PHE* 3.5 6.1 - - + +
290F MET* 4.1 33.2 - - + -
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Residues in contact with GLY 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL 3.6 5.6 - - - -
20F VAL 3.7 2.6 - - - +
23F GLY* 3.8 7.3 - - - -
24F PRO* 3.6 17.7 - - - +
27F MET* 4.0 5.4 - - - +
95F LEU* 1.3 77.2 - - - +
97F GLY* 1.3 63.9 + - - -
101F ILE* 3.6 16.0 - - - +
269F PHE 3.1 12.6 + - - -
270F VAL* 4.0 2.2 - - - -
271F GLU 3.7 11.9 + - - -
272F VAL 4.0 1.0 + - - -
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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