Contacts of the strand formed by residues 251 - 259 (chain B) in PDB entry 6QPA
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 THR 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B HIS 3.6 0.2 - - - +
166B TRP* 3.4 2.1 - - - -
167B VAL* 2.9 32.4 + - - +
169B ASP* 6.3 0.2 - - - +
172B GLU* 2.7 26.7 + - + +
200B LYS* 4.0 23.2 - - + -
201B GLN 4.2 8.1 - - - +
248B GLN 3.7 10.3 + - - +
249B THR* 3.7 6.5 - - - +
250B PRO* 1.3 70.5 - - - +
252B GLN* 1.3 69.5 + - - +
253B TYR* 3.5 27.2 + - + -
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Residues in contact with GLN 252 (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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12B MET* 4.7 8.3 - - - +
117B PRO* 4.9 0.5 - - - +
119B PHE* 3.5 14.1 - - + -
164B ASP* 3.1 39.6 + - - +
165B HIS 3.4 4.5 - - - +
166B TRP* 4.2 8.7 - - + +
200B LYS* 3.8 2.1 - - - -
201B GLN* 2.7 66.4 + - + +
248B GLN* 4.0 22.0 + - - +
250B PRO 3.3 2.8 + - - -
251B THR* 1.3 77.9 - - - +
253B TYR* 1.3 61.9 + - - +
254B LEU* 3.7 20.0 - - + +
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Residues in contact with TYR 253 (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 VAL* 4.3 2.5 - - + -
163B GLY 3.5 2.4 - - - +
165B HIS* 2.8 35.7 + - - +
167B VAL* 3.5 27.8 - - + -
172B GLU* 3.3 27.4 - - + +
175B PHE* 3.4 31.2 - + + -
176B GLU* 2.5 43.4 + - + +
198B ILE* 4.1 9.9 - - + -
199B MET 3.1 14.1 - - - +
200B LYS* 3.3 27.7 - - + -
251B THR* 3.5 19.3 - - + -
252B GLN* 1.3 77.0 - - - +
254B LEU* 1.3 65.2 + - - +
255B VAL* 4.0 0.7 - - + -
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Residues in contact with LEU 254 (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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10B ILE* 3.8 15.0 - - + -
12B MET* 3.6 19.7 - - + -
77B PHE* 5.0 3.1 - - + -
119B PHE* 3.4 34.7 - - + -
162B ILE* 4.0 22.9 - - + -
163B GLY 3.4 1.1 - - - -
164B ASP* 3.9 19.1 - - + +
197B MET 3.8 0.2 - - - +
199B MET* 2.9 50.6 + - + +
252B GLN* 3.7 24.0 - - - +
253B TYR* 1.3 76.0 - - - +
255B VAL* 1.3 63.3 + - - +
256B HIS 3.7 2.1 + - - -
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Residues in contact with VAL 255 (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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161B VAL 3.6 1.7 - - - +
162B ILE* 3.4 4.3 - - - -
163B GLY* 2.8 34.1 + - - +
165B HIS* 3.5 31.2 - - + +
175B PHE* 4.3 16.6 - - + -
179B ALA* 4.8 5.8 - - + -
183B LEU* 3.8 24.0 - - + -
197B MET 3.7 3.6 - - - +
198B ILE* 4.7 13.5 - - + -
253B TYR 5.0 0.2 - - - +
254B LEU* 1.3 72.6 - - - +
256B HIS* 1.3 61.2 + - - +
257B ILE* 3.7 27.5 + - + +
296B TYR* 4.1 7.9 - - - +
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Residues in contact with HIS 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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46B GLU* 5.6 4.9 - - + -
48B LEU* 4.9 2.0 - - + -
79B TYR* 2.7 39.9 + + - +
126B LEU* 4.3 10.5 - - + +
160B VAL* 3.6 22.1 - - + +
161B VAL 3.5 4.9 - - - -
162B ILE* 4.7 2.4 - - + +
196B TRP* 3.0 6.2 - - - +
197B MET* 2.8 60.4 + - + +
199B MET* 3.8 17.5 - - + -
254B LEU 3.7 0.4 + - - -
255B VAL* 1.3 71.5 - - - +
257B ILE* 1.3 63.4 + - - +
258B GLU* 2.7 39.9 + - + +
308B TRP* 5.9 0.9 - + - -
309B ARG* 4.4 1.8 + - - -
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Residues in contact with ILE 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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160B VAL* 3.7 0.5 - - - -
161B VAL* 2.8 42.6 + - + +
183B LEU* 3.6 22.9 - - + -
186B MET* 4.6 5.6 - - + -
193B MET* 3.8 18.6 - - + -
195B GLY 3.4 11.0 - - - +
196B TRP* 4.5 1.6 - - + -
255B VAL* 3.7 21.5 - - + +
256B HIS* 1.3 80.0 - - - +
258B GLU* 1.3 65.9 + - - +
259B TRP* 3.3 28.4 - - + +
269B LEU* 3.8 27.6 - - + -
296B TYR* 4.2 9.6 - - + +
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Residues in contact with GLU 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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46B GLU* 5.5 0.2 - - - -
126B LEU* 3.6 13.1 - - + +
158B ARG* 2.8 36.0 + - - +
159B THR 3.3 7.2 - - - +
160B VAL* 4.2 8.6 - - + +
193B MET 3.8 0.5 - - - -
194B VAL* 2.8 41.6 + - + +
195B GLY 2.8 13.1 + - - +
256B HIS* 2.7 33.7 + - + +
257B ILE* 1.3 76.2 - - - +
259B TRP* 1.3 65.3 + - - +
309B ARG* 2.3 36.9 + - - -
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Residues in contact with TRP 259 (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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158B ARG* 3.4 6.6 - - - +
159B THR* 2.8 27.4 + - - +
161B VAL* 4.2 10.8 - - + +
186B MET* 3.3 32.3 - - + -
190B VAL* 3.7 10.3 - - + -
191B PRO 3.7 10.3 - - - -
192B GLY 3.3 22.9 - - - -
193B MET* 3.5 28.3 - - + -
194B VAL* 3.8 6.1 - - - -
257B ILE* 3.3 30.2 - - + +
258B GLU* 1.3 78.0 - - - +
260B GLU* 1.3 67.1 + - - +
261B SER 3.7 7.6 - - - +
264B HIS 3.5 20.4 - - - -
265B ALA* 3.3 36.4 - - + +
268B GLY* 3.5 15.5 - - - -
269B LEU* 4.0 15.8 - - + +
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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