Contacts of the strand formed by residues 251 - 259 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C HIS 3.7 0.2 - - - +
166C TRP* 3.5 1.6 - - - -
167C VAL* 2.9 33.4 + - - +
172C GLU* 2.8 30.3 + - + +
200C LYS* 4.0 23.0 - - + -
201C GLN 4.3 7.9 - - - +
248C GLN 3.7 9.4 + - - +
249C THR* 3.8 6.8 - - - +
250C PRO* 1.3 71.2 - - - +
252C GLN* 1.3 68.2 + - - +
253C TYR* 3.6 24.2 + - + -
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Residues in contact with GLN 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C MET* 4.7 8.4 - - - +
117C PRO* 5.0 0.5 - - - +
119C PHE* 3.6 13.6 - - + -
164C ASP* 2.9 39.1 + - - +
165C HIS 3.4 4.3 - - - +
166C TRP* 4.1 8.7 - - + +
200C LYS* 3.8 2.3 - - - -
201C GLN* 2.8 65.2 + - + +
248C GLN* 4.1 22.6 + - - +
250C PRO 3.3 2.8 + - - -
251C THR* 1.3 76.9 - - - +
253C TYR* 1.3 69.6 + - - +
254C LEU* 3.7 15.5 + - + +
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Residues in contact with TYR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 4.2 3.1 - - + -
163C GLY 3.4 2.4 - - - +
165C HIS* 2.9 35.9 + - + +
167C VAL* 3.5 28.9 - - + -
172C GLU* 3.4 25.9 - - + +
175C PHE* 3.4 32.5 - + + -
176C GLU* 2.7 43.6 + - + +
198C ILE* 4.0 10.3 - - + -
199C MET 3.2 15.5 - - - +
200C LYS* 3.5 29.0 - - + -
251C THR* 3.6 18.6 - - + -
252C GLN* 1.3 77.0 - - - +
254C LEU* 1.3 66.1 + - - +
255C VAL* 5.2 0.2 - - + -
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.9 14.1 - - + -
12C MET* 3.7 19.3 - - + -
77C PHE* 4.8 5.2 - - + -
119C PHE* 3.6 34.3 - - + -
162C ILE* 3.9 25.1 - - + -
163C GLY 3.4 1.3 - - - -
164C ASP* 3.8 24.7 - - + +
198C ILE* 3.9 0.7 - - - +
199C MET* 2.9 44.7 + - + +
252C GLN* 3.7 22.9 - - - +
253C TYR* 1.3 72.5 - - - +
255C VAL* 1.3 62.6 + - - +
256C HIS 3.7 1.6 + - - -
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C VAL 3.4 2.8 - - - +
162C ILE* 3.4 4.8 - - - -
163C GLY 2.9 33.5 + - - +
165C HIS* 3.5 31.0 - - + +
175C PHE* 4.2 18.2 - - + -
179C ALA* 4.9 5.8 - - + -
183C LEU* 3.8 24.2 - - + -
197C MET 3.7 3.6 - - - +
198C ILE* 4.9 12.1 - - + +
253C TYR 5.1 0.7 - - - +
254C LEU* 1.3 72.8 - - - +
256C HIS* 1.3 58.9 + - - +
257C ILE* 3.7 28.1 + - + +
296C TYR* 4.3 6.5 - - - +
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Residues in contact with HIS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 5.6 5.4 - - + -
48C LEU* 4.9 2.0 - - + -
79C TYR* 2.8 39.0 + + - +
126C LEU* 4.1 13.4 - - + +
160C VAL* 3.5 22.6 - - + +
161C VAL 3.5 4.9 - - - -
162C ILE* 4.7 1.8 - - - +
196C TRP* 3.0 6.1 - - - +
197C MET* 2.7 60.7 + - + +
199C MET* 3.9 17.0 - - + -
254C LEU 3.7 1.0 + - - -
255C VAL* 1.3 70.7 - - - +
257C ILE* 1.3 61.1 + - - +
258C GLU* 2.8 38.9 + - + +
308C TRP* 5.8 0.9 - + - -
309C ARG* 4.4 2.9 + - - -
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Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL* 3.6 0.5 - - - -
161C VAL* 2.8 43.3 + - + +
183C LEU* 3.7 21.3 - - + -
186C MET* 4.8 5.6 - - + -
193C MET* 3.8 19.7 - - + -
195C GLY 3.4 10.3 - - - +
196C TRP* 4.4 0.4 - - + -
255C VAL* 3.7 22.4 - - + +
256C HIS* 1.3 79.0 - - - +
258C GLU* 1.3 63.8 + - - +
259C TRP* 3.3 29.4 - - + +
269C LEU* 3.7 27.8 - - + -
296C TYR* 4.1 11.0 - - + +
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 3.6 11.4 - - + +
153C ALA* 4.3 0.2 - - - +
158C ARG* 3.0 28.4 + - - +
159C THR 3.3 6.1 - - - +
160C VAL* 4.1 10.7 - - + +
193C MET* 3.8 0.9 - - - -
194C VAL* 2.8 46.3 + - + +
195C GLY 2.7 17.8 + - - +
256C HIS* 2.8 31.1 + - + +
257C ILE* 1.3 74.7 - - - +
259C TRP* 1.3 62.7 + - - +
309C ARG* 2.3 42.3 + - - -
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Residues in contact with TRP 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ARG* 3.3 7.1 - - - +
159C THR* 2.7 28.4 + - - +
161C VAL* 4.1 10.8 - - + +
186C MET* 3.4 34.8 - - + -
190C VAL* 3.7 11.2 - - + -
191C PRO 3.6 15.3 - - - -
192C GLY 3.3 23.1 - - - -
193C MET* 3.6 18.2 - - + -
194C VAL* 3.8 5.6 - - - -
257C ILE* 3.3 35.8 - - + +
258C GLU* 1.3 79.4 - - - +
260C GLU* 1.3 65.7 + - - +
261C SER 3.2 3.6 - - - +
264C HIS 3.4 19.5 - - - -
265C ALA* 3.4 41.0 - - + +
268C GLY* 3.5 11.9 - - - -
269C LEU* 4.0 15.7 - - + +
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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