Contacts of the strand formed by residues 255 - 260 (chain A) in PDB entry 6R4E
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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10A TYR* 2.9 40.8 + - + +
12A VAL* 3.8 4.6 - - - +
211A VAL* 3.9 12.1 - - + -
212A ARG 3.5 13.9 - - - +
213A SER* 4.1 7.4 - - - +
217A LEU* 4.9 1.6 - - + -
249A PRO* 3.9 12.1 - - + -
253A LYS 3.4 13.5 - - - +
254A ALA* 1.3 75.6 - - - +
256A GLU* 1.3 75.7 + - - +
257A TYR* 3.7 35.2 - - + +
287A GLY 3.7 12.8 - - - +
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Residues in contact with GLU 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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7A TYR* 2.3 39.2 + - + +
8A LEU 3.3 5.4 - - - +
9A ASN* 4.3 3.8 - - - -
12A VAL* 4.0 22.2 - - + +
14A ARG* 2.9 18.9 + - - -
211A VAL* 3.4 4.2 - - - -
212A ARG* 2.8 71.6 + - + +
255A VAL* 1.3 81.5 - - - +
257A TYR* 1.3 62.7 + - - +
258A TYR* 3.7 15.4 - - + +
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Residues in contact with TYR 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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6A ALA 3.9 0.2 - - - +
7A TYR* 3.6 3.6 - - - -
8A LEU* 2.9 52.0 + - + +
10A TYR* 5.2 0.4 - - + -
209A ILE* 4.3 11.7 - - + -
210A GLY 3.3 10.1 - - - +
211A VAL* 4.0 19.0 - - + +
247A LEU* 3.4 21.7 + - + +
248A PHE* 4.3 2.1 - - - -
255A VAL* 3.7 23.9 - - + +
256A GLU* 1.3 77.2 - - - +
258A TYR* 1.3 66.8 + - - +
259A PHE* 4.2 14.6 - - + -
284A VAL* 3.8 26.9 - - + -
287A GLY* 2.8 31.4 + - - -
289A LEU* 3.7 26.0 + - + -
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Residues in contact with TYR 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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5A PHE* 4.0 15.9 - + + -
6A ALA 3.3 6.3 - - - +
7A TYR* 3.4 29.6 - + - -
22A THR* 4.7 0.9 - - + -
208A LEU 3.8 0.3 - - - +
209A ILE* 3.2 4.9 - - - -
210A GLY 2.7 51.8 + - - +
212A ARG* 3.1 36.9 + - + -
256A GLU* 3.6 27.0 + - + -
257A TYR* 1.3 75.0 - - - +
259A PHE* 1.3 62.5 + - - +
260A ALA 3.9 0.2 + - - -
266A VAL* 3.9 22.4 - - + +
269A HIS* 3.4 44.4 + + + +
270A THR* 4.1 12.3 - - + -
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Residues in contact with PHE 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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4A ILE* 4.9 0.9 - - - -
5A PHE* 3.3 5.8 - - - -
6A ALA* 2.9 52.3 + - + +
8A LEU* 5.2 3.6 - - + -
89A LEU* 5.5 1.6 - - + -
188A VAL* 4.2 24.2 - - + -
198A ALA* 3.8 30.7 - - + -
199A VAL 4.7 0.7 - - - -
200A GLY* 4.0 24.9 - - - -
207A LEU* 4.8 7.4 - - + -
208A LEU 3.5 5.6 - - - +
209A ILE* 3.5 37.2 - - + -
257A TYR* 4.6 12.1 - - + -
258A TYR* 1.3 75.2 - - - +
260A ALA* 1.3 63.7 + - - +
282A ALA* 4.7 3.6 - - + -
284A VAL* 4.1 21.1 - - + -
289A LEU* 5.1 0.7 - - + -
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Residues in contact with ALA 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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4A ILE* 3.3 14.4 - - - +
5A PHE* 4.3 7.4 - - + -
207A LEU* 3.5 8.8 - - - +
208A LEU* 2.8 38.8 + - + +
258A TYR 3.9 0.2 + - - -
259A PHE* 1.3 78.4 - - - +
261A SER* 1.3 60.8 + - - +
262A ASP 3.4 20.4 - - - +
265A ALA* 4.3 2.7 - - + -
266A VAL* 3.6 22.4 - - + -
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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