Contacts of the strand formed by residues 264 - 270 (chain F) 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 ILE 264 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91F PHE* 3.7 18.9 - - + -
119F ILE* 4.2 6.3 - - + -
221F VAL* 3.4 29.2 - - + +
223F LEU* 4.1 16.4 - - + -
258F LEU* 4.1 40.6 + - + +
262F GLN* 3.7 2.4 - - - +
263F ILE* 1.3 83.4 - - + +
265F THR* 1.3 58.7 + - - +
266F SER 3.3 27.4 - - - +
267F ALA* 4.5 1.3 - - + -
293F LEU* 4.1 16.8 - - + -
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Residues in contact with THR 265 (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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2F LYS* 6.1 0.3 - - - +
91F PHE* 3.3 21.5 - - - -
92F PRO* 3.9 7.1 - - - +
113F TYR* 3.3 30.1 + - + +
116F LEU* 4.2 3.3 - - - +
219F ASP 4.9 1.6 - - - +
220F GLY* 3.4 15.5 - - - -
221F VAL 2.7 33.8 + - - -
263F ILE 3.9 9.2 - - - +
264F ILE* 1.3 75.4 - - - +
266F SER* 1.3 59.4 + - - -
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Residues in contact with SER 266 (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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91F PHE* 3.4 10.1 - - - -
92F PRO* 3.6 23.8 - - - -
105F THR* 5.5 0.4 - - - -
109F VAL* 3.7 22.6 - - - +
221F VAL 3.5 1.0 + - - -
222F HIS* 2.7 36.3 + - - +
223F LEU 2.9 22.5 + - - -
264F ILE* 3.3 5.5 - - - +
265F THR* 1.3 79.3 + - - +
267F ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 267 (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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91F PHE* 3.4 16.9 - - + -
92F PRO 3.2 11.1 + - - +
93F LEU* 3.5 5.6 - - + -
94F VAL* 3.0 23.4 + - - +
105F THR* 4.9 0.5 - - - +
222F HIS* 3.9 5.2 + - - -
223F LEU* 3.2 22.9 - - + +
264F ILE* 4.5 0.2 - - + -
266F SER* 1.3 79.3 - - - +
268F GLU* 1.3 63.0 + - - +
269F PHE* 4.2 8.7 - - + -
293F LEU* 4.0 17.5 - - + -
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Residues in contact with GLU 268 (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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94F VAL* 3.0 23.1 - - + +
101F ILE* 3.9 5.7 - - - +
102F ALA* 3.3 28.0 + - - +
105F THR* 2.7 29.4 + - - -
222F HIS* 2.7 27.0 + - + +
223F LEU 3.0 5.9 + - - +
224F SER* 2.8 24.3 + - - +
225F LEU* 2.9 28.6 + - - +
267F ALA* 1.3 75.9 - - - +
269F PHE* 1.3 65.7 + - - +
270F VAL* 4.1 13.0 - - + -
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Residues in contact with PHE 269 (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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27F MET* 3.6 15.3 - - - +
93F LEU* 4.2 13.7 - - + -
94F VAL 3.1 6.7 + - - -
95F LEU* 3.8 2.8 - - + -
96F GLY 3.0 22.3 + - - -
223F LEU* 4.3 11.7 - - + -
225F LEU* 3.3 38.6 - - + -
227F LEU* 4.3 13.5 - - + -
255F MET* 4.6 3.6 - - - -
267F ALA* 4.2 7.2 - - + -
268F GLU* 1.3 74.9 - - - +
270F VAL* 1.3 60.4 + - - +
286F ALA* 4.2 8.1 - - + -
289F LEU* 4.0 15.0 - - + -
290F MET* 3.4 52.7 - - + -
293F LEU* 4.2 24.5 - - + -
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Residues in contact with VAL 270 (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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96F GLY* 4.5 1.8 - - - +
97F GLY 3.4 7.9 - - - +
98F ASP 4.4 0.7 - - - +
99F HIS* 3.7 37.2 - - + +
101F ILE* 3.8 34.5 - - + -
225F LEU 2.9 6.1 + - - +
226F ASP* 3.5 21.8 - - + -
227F LEU* 3.1 24.8 + - - +
268F GLU* 4.1 16.6 - - + -
269F PHE* 1.3 79.4 - - - +
271F GLU* 1.3 72.5 + - + +
272F VAL* 3.3 5.0 + - - -
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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