Contacts of the strand formed by residues 255 - 259 (chain A) in PDB entry 3CB4
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 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASN* 3.8 19.3 - - - +
58A SER* 5.2 3.8 - - - +
59A VAL 6.2 0.2 - - - +
60A THR* 3.6 11.8 + - - +
72A GLN* 4.8 0.5 + - - -
74A ASN* 3.9 19.0 - - + +
76A ILE* 3.9 24.2 - - + -
196A ILE* 4.2 6.7 - - + -
209A LEU* 3.8 24.5 - - + -
210A ILE 3.1 10.1 - - - +
211A ARG* 3.9 19.7 - - + -
239A ILE* 3.6 18.0 - - - +
250A LEU* 4.1 4.3 - - - +
254A GLU* 1.3 80.6 - - - +
256A GLY* 1.3 60.4 + - - +
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Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.4 13.4 - - - +
210A ILE* 2.7 40.3 + - - +
238A GLY 3.1 14.1 - - - -
239A ILE* 4.3 4.5 - - - -
240A PHE 5.3 1.3 - - - -
250A LEU* 3.8 13.7 - - - +
255A VAL* 1.3 76.6 - - - +
257A TRP* 1.3 59.6 + - - -
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Residues in contact with TRP 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TRP* 4.7 0.7 - - + -
204A LEU* 5.2 1.3 - - + -
207A VAL* 3.9 11.4 - - + -
208A SER 3.1 9.0 - - - +
236A ARG* 3.7 31.6 - - + -
237A LEU* 3.1 13.8 - - - +
238A GLY* 2.8 45.5 + - - +
239A ILE 3.2 23.2 + - - -
240A PHE* 3.5 39.0 - + + -
244A GLN* 3.6 28.7 - - + +
245A VAL 3.5 11.3 + - - -
246A ASP* 3.2 34.8 - - - -
250A LEU* 4.0 2.9 - - - +
256A GLY* 1.3 74.7 - - - -
258A LEU* 1.3 64.4 + - - +
259A VAL* 3.8 23.3 - - + -
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL 4.0 0.9 - - - +
207A VAL* 3.6 7.1 - - - -
208A SER* 2.9 33.0 + - - +
210A ILE* 3.6 17.3 - - + -
217A LEU* 4.0 14.6 - - + -
223A VAL* 4.8 7.2 - - + -
234A ALA* 3.7 29.4 - - + -
236A ARG 3.5 13.7 - - - +
237A LEU* 4.0 11.4 - - + -
250A LEU* 5.8 0.9 - - + -
257A TRP* 1.3 75.7 - - - +
259A VAL* 1.3 64.0 + - - +
260A CYS* 3.9 24.3 + - - -
262A ILE* 6.1 0.4 - - + -
274A LEU* 3.5 31.4 - - + -
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 3.7 42.2 - - + +
206A VAL 4.3 2.7 - - - +
207A VAL* 4.0 17.3 - - + -
234A ALA 3.9 0.2 - - - -
235A ASP* 3.1 14.7 + - + +
236A ARG* 2.6 48.9 + - + +
257A TRP* 3.8 22.0 - - + -
258A LEU* 1.3 80.2 - - - +
260A CYS* 1.3 67.0 - - - +
261A ALA* 5.9 0.4 - - - -
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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