Contacts of the strand formed by residues 263 - 267 (chain B) in PDB entry 5H1C
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 VAL 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 5.3 0.7 - - - +
121B SER 2.8 24.5 + - - +
122B ILE* 3.6 21.5 - - + -
123B THR* 2.9 29.2 + - - +
219B LEU* 3.6 13.7 - - + +
221B VAL* 6.0 2.9 - - + -
252B LEU* 4.3 34.3 - - + +
255B LEU* 6.1 0.7 - - + -
256B ALA* 3.4 29.6 - - + -
260B GLY 5.6 0.4 - - - +
262B ALA* 1.3 78.2 - - - +
264B VAL* 1.3 66.3 + - - +
265B ILE* 4.8 3.1 - - + -
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 5.0 6.5 - - + -
123B THR* 3.2 13.0 - - - +
125B MET* 4.3 23.3 - - + -
137B CYS* 4.5 17.0 - - - -
140B LEU* 4.7 13.7 - - + -
218B LEU* 3.3 37.2 - - + -
219B LEU 3.1 8.5 + - - +
220B ILE* 4.1 9.9 - - + -
221B VAL* 2.9 31.7 + - - +
262B ALA* 5.1 0.7 - - + -
263B VAL* 1.3 76.5 - - - +
265B ILE* 1.3 70.1 + - - +
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Residues in contact with ILE 265 (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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122B ILE* 2.9 31.6 - - + -
123B THR 2.8 18.3 + - - +
124B GLU* 3.1 12.7 - - + +
125B MET* 2.8 27.6 + - - +
221B VAL* 3.6 3.1 - - + +
224B ALA* 4.1 25.1 - - + -
225B THR* 5.3 3.6 - - + -
249B LEU* 4.3 23.3 - - + -
252B LEU* 4.4 11.4 - - + -
263B VAL* 4.8 3.6 - - + -
264B VAL* 1.3 81.7 - - - +
266B THR* 1.3 64.8 + - - +
267B ASN* 3.4 16.0 - - - +
292B ILE* 5.8 4.0 - - + -
296B SER* 5.8 0.2 - - - -
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Residues in contact with THR 266 (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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125B MET* 3.2 27.5 - - + +
133B LYS* 3.3 38.6 - - + -
134B THR 4.8 0.7 - - - +
137B CYS* 3.9 11.4 - - - -
221B VAL 2.8 14.9 + - - -
222B ASP* 2.2 50.4 + - - +
223B SER* 3.6 11.4 - - - -
224B ALA 3.9 4.3 + - - -
225B THR* 4.1 3.1 + - - +
264B VAL* 5.2 0.2 - - - +
265B ILE* 1.3 74.9 - - - +
267B ASN* 1.3 64.0 + - - +
268B GLN* 6.0 0.2 - - - -
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Residues in contact with ASN 267 (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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124B GLU* 2.5 40.6 + - - +
125B MET 3.1 20.5 + - - +
126B PHE* 4.2 6.7 - - + -
127B GLY 4.2 10.7 + - - +
133B LYS* 4.7 8.4 - - - -
225B THR* 4.0 12.7 - - + +
265B ILE* 3.4 18.6 - - - +
266B THR* 1.3 82.9 - - - +
268B GLN* 1.3 72.3 + - - +
269B VAL* 4.3 0.5 - - - +
286B PRO* 4.3 13.1 - - + +
287B ILE* 5.2 2.5 - - + +
292B ILE* 3.9 15.0 - - - +
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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