Contacts of the strand formed by residues 258 - 262 (chain A) in PDB entry 3RC0
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 ALA 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.9 9.9 - - + -
250A LEU* 4.4 1.6 - - + -
256A HIS* 3.1 19.9 - - - -
257A ASN* 1.3 81.3 - - - +
259A ASN* 1.3 62.2 + - - +
269A MET* 4.3 11.4 - - - -
270A VAL 3.3 11.9 - - - +
272A THR* 3.5 3.9 + - - +
281A ILE* 3.7 26.5 - - + -
282A PHE 3.0 14.0 + - - +
283A ASN* 3.5 9.4 - - - +
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Residues in contact with ASN 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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256A HIS* 4.5 5.5 + - + -
258A ALA* 1.3 77.5 - - - +
260A LEU* 1.3 65.9 + - - +
261A GLU* 4.5 12.4 - - - +
268A ARG 3.7 0.5 - - - +
269A MET* 3.5 6.1 - - - -
270A VAL* 3.0 33.4 + - - +
272A THR* 3.5 23.1 - - + +
283A ASN* 3.8 6.7 - - - -
284A THR* 4.3 10.0 - - + +
312P ILE* 3.9 11.0 - - + -
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Residues in contact with LEU 260 (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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90A PHE* 5.5 1.6 - - + -
92A VAL* 5.9 0.9 - - + -
225A PHE* 3.6 32.1 - - + -
247A ALA* 4.5 7.9 - - + -
259A ASN* 1.3 77.2 + - - +
261A GLU* 1.3 68.9 + - - +
262A TYR* 3.8 15.7 - - + +
267A LEU* 3.6 39.7 - - + -
268A ARG 3.4 18.6 - - - +
269A MET* 3.7 22.1 - - + +
312P ILE* 3.0 43.2 - - + +
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Residues in contact with GLU 261 (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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259A ASN* 4.5 10.2 - - - +
260A LEU* 1.3 79.5 - - - +
262A TYR* 1.3 66.6 + - - +
263A SER* 4.1 2.4 + - - +
267A LEU* 3.4 5.4 - - - +
268A ARG* 2.8 52.0 + - + +
270A VAL* 3.7 31.4 - - + +
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Residues in contact with TYR 262 (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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94A ARG* 3.7 14.8 - - - +
97A LEU* 6.0 1.1 - - + -
225A PHE* 3.7 21.4 - - + +
227A GLU* 3.3 48.9 + - + +
228A PRO* 3.8 18.6 - - + -
242A VAL* 5.7 4.2 - - + +
260A LEU* 3.8 11.1 - - + +
261A GLU* 1.3 79.1 - - - +
263A SER* 1.3 64.1 + - - +
266A CYS 4.0 2.2 - - - -
267A LEU* 3.8 25.8 - - + +
311P SER 2.8 29.6 + - - -
312P ILE 3.9 12.8 - - - -
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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