Contacts of the strand formed by residues 264 - 268 (chain F) in PDB entry 5IC4
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 CYS 264 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164E ARG* 3.6 17.5 - - - +
195F TYR 3.5 2.4 - - - +
197F TYR* 3.0 36.9 + - + +
199F THR 3.4 21.5 - - - +
200F ALA* 4.0 1.1 - - - -
201F PRO* 4.0 8.5 - - - -
263F PRO* 1.3 74.9 - - - +
265F ILE* 1.3 61.5 + - - +
266F VAL* 3.9 10.3 - - - -
266H VAL* 3.6 31.2 - - - -
267H SER 3.9 3.4 - - - -
268H MET* 3.6 14.6 - - - -
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Residues in contact with ILE 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F LEU* 3.9 9.0 - - + -
195F TYR 3.9 3.4 - - - +
196F ALA* 4.9 3.8 - - + +
233F MET* 3.6 31.4 - - + +
236F LEU* 3.6 51.1 - - + +
237F THR* 4.0 8.5 - - - +
240F ASN* 3.5 29.6 - - - +
263F PRO* 5.7 0.4 - - + -
264F CYS* 1.3 71.2 - - - +
266F VAL* 1.3 62.1 + - - +
233H MET* 5.5 0.4 - - + -
265H ILE 3.1 5.4 - - - +
266H VAL* 3.2 2.6 - - - +
267H SER* 2.8 50.1 + - - +
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Residues in contact with VAL 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ARG* 5.3 2.0 - - - +
194F LEU* 3.3 2.4 - - - +
195F TYR* 2.8 65.1 + - + +
197F TYR* 3.7 25.1 - - + -
264F CYS* 3.9 15.3 - - - -
265F ILE* 1.3 75.6 - - - +
267F SER* 1.3 60.6 + - - +
268F MET* 4.2 5.2 - - + -
201H PRO* 5.7 3.8 - - + -
264H CYS* 3.7 27.4 - - - -
265H ILE 3.2 2.7 - - - -
266H VAL* 3.9 11.0 - - + -
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Residues in contact with SER 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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194F LEU* 3.6 15.0 - - - -
233F MET* 3.6 26.0 - - - +
266F VAL* 1.3 72.5 - - - +
268F MET* 1.3 60.9 + - - +
269F LEU* 3.3 27.8 + - - +
237H THR* 5.3 2.4 + - - -
240H ASN* 3.5 8.5 + - - -
264H CYS* 3.9 1.9 - - - -
265H ILE* 2.7 47.3 + - - +
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Residues in contact with MET 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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137E LYS* 5.8 1.8 - - - +
190F GLU* 3.4 34.3 - - - +
191F ALA* 3.5 3.5 - - - -
192F ASP 2.7 27.4 + - - -
193F PHE* 2.7 18.1 + - + +
195F TYR* 3.5 35.0 - - + +
266F VAL* 4.2 4.3 - - + -
267F SER* 1.3 71.9 - - - +
269F LEU* 1.3 57.9 + - - +
270F THR 3.9 0.2 + - - -
200H ALA* 4.1 18.4 - - + -
201H PRO* 4.3 8.7 - - + -
240H ASN* 4.0 5.8 - - - +
262H ILE* 3.9 17.2 - - + +
263H PRO 3.4 19.1 - - - +
264H CYS* 3.9 26.0 - - + -
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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