Contacts of the strand formed by residues 255 - 260 (chain B) in PDB entry 2XH1
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B TYR* 3.9 13.2 - - + -
227B ILE* 3.4 17.7 - - + +
229B GLU* 4.1 10.8 - - + +
246B PHE* 3.9 23.3 - - + +
247B LEU* 4.0 27.1 - - + +
250B ASP* 3.1 37.2 + - + +
253B GLY 3.6 0.4 - - - -
254B ARG* 1.3 81.4 - - - +
256B ILE* 1.3 74.2 + - - +
257B ARG 4.1 1.3 - - - +
275B THR 4.2 0.5 - - - +
276B GLY* 3.7 5.7 - - - -
277B PRO* 3.3 19.3 - - - +
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Residues in contact with ILE 256 (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 VAL* 3.9 33.4 - - + -
127B MET* 4.4 9.2 - - + -
128B ILE* 4.4 8.3 - - + -
226B LEU* 4.5 8.5 - - + -
227B ILE 3.0 9.3 + - - +
228B ILE* 3.4 18.2 - - + +
229B GLU 2.8 25.5 + - - -
254B ARG 4.0 2.0 + - - +
255B VAL* 1.3 76.9 - - - +
257B ARG* 1.3 61.5 + - - +
274B LEU* 3.8 29.6 - - + -
275B THR 3.6 9.0 - - - +
276B GLY* 4.5 0.2 - - - -
277B PRO* 4.1 14.6 - - + -
280B LEU* 4.0 23.8 - - + -
281B ILE* 5.0 4.3 - - + -
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Residues in contact with ARG 257 (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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91B GLN* 4.1 2.9 - - - +
95B HIS* 3.9 12.3 + - - -
229B GLU* 3.1 43.8 + - + +
231B ASP* 2.8 35.7 + - - +
234B TYR* 3.3 26.1 - - - +
245B THR* 3.4 11.9 - - - +
247B LEU* 3.8 27.6 - - + -
255B VAL* 4.1 4.4 - - + -
256B ILE* 1.3 74.7 - - - +
258B ALA* 1.3 62.4 + - - +
259B ASP* 2.7 39.5 + - - +
273B PHE 4.0 0.5 - - - +
274B LEU* 3.5 7.4 - - - +
275B THR* 2.8 47.6 + - - +
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Residues in contact with ALA 258 (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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117B SER* 4.4 18.4 - - - +
121B LEU* 3.8 28.3 - - + -
228B ILE* 5.0 0.8 - - - +
229B GLU 2.9 9.2 + - - +
230B ASP* 4.3 9.4 - - - +
231B ASP* 3.1 28.4 + - - +
232B PRO 4.5 0.3 - - - -
256B ILE 4.2 0.4 + - - -
257B ARG* 1.3 73.7 - - - +
259B ASP* 1.3 60.7 + - - +
273B PHE 3.6 6.1 - - - +
274B LEU* 4.1 10.8 - - + -
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Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 3.2 20.3 + - - +
95B HIS* 5.2 0.7 + - - -
117B SER* 3.2 12.0 - - - -
231B ASP 4.2 8.5 - - - +
232B PRO* 5.2 0.2 - - - -
234B TYR* 4.5 1.6 - - - +
235B PHE* 4.4 14.6 - - - -
257B ARG* 2.7 46.8 + - - +
258B ALA* 1.3 74.5 - - - +
260B SER* 1.3 61.2 + - - +
273B PHE* 2.9 60.8 + - + -
275B THR* 4.7 0.7 + - - -
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Residues in contact with SER 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.8 7.2 - - - -
231B ASP 4.9 0.4 + - - -
232B PRO* 4.0 35.0 - - - +
235B PHE* 5.1 7.6 - - - -
259B ASP* 1.3 77.2 + - - +
261B PHE* 1.3 62.4 + - - +
262B SER* 2.8 27.9 + - - -
263B LYS* 4.5 2.7 + - - +
264B ILE* 4.5 9.4 - - - +
271B ILE 5.0 0.3 + - - -
272B GLY* 4.5 3.1 - - - -
273B PHE* 4.8 4.0 - - - -
1427B PLP 2.7 28.8 + - - -
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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