Contacts of the strand formed by residues 264 - 270 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C PHE* 3.6 19.3 - - + -
119C ILE* 4.1 7.4 - - + -
221C VAL* 3.4 28.3 - - + +
223C LEU* 4.0 17.5 - - + -
258C LEU* 3.8 43.0 + - + +
262C GLN* 4.7 1.4 - - - +
263C ILE* 1.3 83.2 + - + +
265C THR* 1.3 58.1 + - - +
266C SER 3.4 26.2 - - - +
267C ALA* 4.4 1.6 - - + -
293C LEU* 4.0 17.5 - - + -
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Residues in contact with THR 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LYS* 6.1 0.2 - - - +
91C PHE* 3.3 21.0 - - - -
92C PRO* 3.9 8.1 - - - +
113C TYR* 3.2 32.1 + - + +
116C LEU* 4.3 2.9 - - - +
219C ASP 5.0 1.3 - - - +
220C GLY* 3.5 14.9 - - - -
221C VAL 2.8 29.2 + - - -
263C ILE 3.3 9.6 + - - +
264C ILE* 1.3 74.1 - - - +
266C SER* 1.3 60.1 + - - -
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Residues in contact with SER 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C PHE* 3.3 10.4 - - - -
92C PRO* 3.5 25.1 - - - -
105C THR* 5.6 0.7 - - - -
109C VAL* 3.7 20.2 - - - +
221C VAL 3.6 1.0 + - - -
222C HIS* 2.7 35.8 + - - +
223C LEU 2.9 22.2 + - - -
264C ILE* 3.4 4.9 - - - +
265C THR* 1.3 81.0 + - - +
267C ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C PHE* 3.5 14.5 - - + -
92C PRO 3.2 10.6 + - - +
93C LEU* 3.5 4.8 - - + -
94C VAL* 2.9 25.5 + - - +
105C THR* 4.9 0.3 - - - +
222C HIS* 3.8 6.3 + - - -
223C LEU* 3.1 23.1 - - + +
264C ILE* 4.4 0.7 - - + -
266C SER* 1.3 78.9 - - - +
268C GLU* 1.3 63.4 + - - +
269C PHE* 4.3 8.5 - - + -
293C LEU* 4.1 17.7 - - + -
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C VAL* 3.0 22.4 - - + +
101C ILE* 4.0 6.6 - - - +
102C ALA* 3.3 28.1 + - - +
105C THR* 2.7 28.4 + - - -
120C TRP* 5.0 0.2 - - - -
222C HIS* 2.8 27.8 + - + +
223C LEU 3.0 5.7 + - - +
224C SER* 2.9 23.6 + - - +
225C LEU* 2.9 27.2 + - - +
267C ALA* 1.3 76.9 - - - +
269C PHE* 1.3 68.9 + - - +
270C VAL* 4.1 13.0 - - + -
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Residues in contact with PHE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C MET* 3.7 17.7 - - - +
93C LEU* 4.2 13.2 - - + -
94C VAL 3.0 7.3 + - - +
95C LEU* 3.8 2.1 - - + -
96C GLY 3.0 22.0 + - - -
223C LEU* 4.3 11.2 - - + -
225C LEU* 3.3 37.5 - - + -
227C LEU* 4.3 11.2 - - + -
255C MET* 4.6 2.9 - - - -
267C ALA* 4.3 5.8 - - + -
268C GLU* 1.3 81.5 - - - +
270C VAL* 1.3 60.8 + - - +
286C ALA* 4.1 13.2 - - + -
289C LEU* 4.2 9.6 - - + -
290C MET* 3.5 50.3 - - + -
293C LEU* 4.1 26.5 - - + -
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C GLY 4.5 1.1 - - - +
97C GLY 3.3 9.4 - - - +
98C ASP 4.3 0.7 - - - +
99C HIS* 3.5 38.1 - - + +
101C ILE* 3.7 35.2 - - + -
225C LEU 2.9 8.7 + - - +
226C ASP* 3.7 17.9 - - - -
227C LEU* 3.2 25.4 + - - +
268C GLU* 4.1 17.7 - - + -
269C PHE* 1.3 79.0 - - - +
271C GLU* 1.3 74.6 + - + +
272C 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