Contacts of the strand formed by residues 174 - 183 (chain B) in PDB entry 2P80
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 LYS 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B TYR* 3.4 8.1 - - - +
173B ASP* 1.3 79.7 - - - +
175B ILE* 1.3 63.5 + - - +
176B TYR* 2.9 37.1 + - + -
234B THR* 2.6 37.5 + - - +
235B ALA* 4.5 0.2 - - - +
239B GLU* 4.0 21.0 + - - +
240B LYS 3.3 0.4 + - - +
241B VAL* 2.9 39.9 - - + -
242B LEU 3.1 21.3 + - - -
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Residues in contact with ILE 175 (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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23B PRO 4.3 0.2 - - - +
25B VAL* 3.8 29.1 + - + +
28B HIS* 4.0 22.7 - - + +
72B LEU* 4.7 2.2 - - + -
155B MET* 3.6 33.9 - - + -
172B TYR* 4.1 15.7 - - + -
174B LYS* 1.3 79.9 - - - +
176B TYR* 1.3 78.2 + - - +
241B VAL* 4.6 0.7 - - - -
242B LEU* 3.2 34.8 - - + +
244B VAL* 4.2 7.2 - - + -
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 3.4 29.4 - - + +
24B PHE* 3.6 35.1 - + - -
25B VAL* 4.7 0.7 - - - -
174B LYS* 2.9 47.1 + - + -
175B ILE* 1.3 85.9 - - - +
177B TYR* 1.3 60.6 + - - +
178B VAL* 4.0 1.3 + - + -
233B MET* 3.9 32.5 - - + -
234B THR* 3.8 15.0 + - - -
241B VAL* 4.2 13.2 - - + -
242B LEU 3.1 5.1 + - - +
243B ILE* 3.4 10.1 - - + +
244B VAL 3.0 24.1 + - - +
320B PHE* 4.4 7.6 - + + -
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 4.1 16.4 - - + +
23B PRO* 2.9 33.9 + - - +
24B PHE 5.0 0.4 - - - +
25B VAL* 4.2 7.2 - - + -
69B PRO* 3.7 16.4 - - + +
70B GLY 3.7 19.3 - - - -
72B LEU* 3.7 33.7 - - + -
152B GLY* 3.3 20.3 - - - -
153B ALA* 3.9 17.5 - - + -
176B TYR* 1.3 72.9 - - - +
178B VAL* 1.3 65.5 + - - +
179B GLY* 3.7 14.7 + - - -
221B ASN* 5.4 0.3 + - - -
244B VAL* 3.4 22.0 - - + -
245B HIS 4.4 0.9 - - - -
246B SER* 2.4 37.7 + - - -
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 4.6 3.6 - - + -
176B TYR* 5.1 1.6 - - + -
177B TYR* 1.3 76.4 - - - +
179B GLY* 1.3 59.2 + - - +
220B PHE* 3.4 40.6 - - + -
221B ASN* 5.1 1.6 - - - +
227B LEU* 3.7 22.7 - - + -
233B MET* 4.4 13.2 - - - -
243B ILE* 4.4 17.0 - - + -
244B VAL 2.8 11.5 + - - +
245B HIS* 3.2 44.1 - - + +
303B TYR* 4.6 9.2 - - + -
318B ALA* 5.8 0.7 - - + -
320B PHE* 4.9 1.6 - - + -
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.1 33.7 - - - +
177B TYR* 3.7 16.7 + - - -
178B VAL* 1.3 72.0 - - - +
180B GLU* 1.3 63.3 + - - -
181B GLN* 4.0 1.0 + - - +
219B VAL 3.8 0.2 - - - +
220B PHE* 3.4 3.1 - - - -
221B ASN* 3.2 25.3 + - - +
222B GLY 4.9 0.5 + - - -
246B SER* 3.8 6.5 - - - -
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Residues in contact with GLU 180 (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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69B PRO* 5.6 0.7 - - - +
151B ASN* 4.8 6.8 - - - +
179B GLY* 1.3 74.6 - - - -
181B GLN* 1.3 68.8 + - - +
218B VAL* 2.6 30.3 - - + +
219B VAL 3.1 7.2 - - - +
220B PHE* 3.0 29.4 - - + -
245B HIS* 2.9 21.4 + - - +
246B SER 3.0 16.0 + - - +
247B GLN* 3.7 26.4 + - + +
250B ARG* 5.4 2.6 - - - +
252B THR* 3.0 28.6 + - - -
305B ASN* 3.9 13.5 + - - +
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Residues in contact with GLN 181 (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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68B VAL* 4.2 13.1 - - + +
69B PRO* 6.2 1.3 - - + -
146B VAL 3.2 16.8 + - - +
147B VAL* 3.2 22.9 + - - +
149B GLY* 3.4 8.2 - - - -
151B ASN* 2.8 30.4 + - - +
179B GLY 5.1 2.0 - - - +
180B GLU* 1.3 78.3 - - - +
182B ASP* 1.3 83.2 + - - +
183B PHE* 3.1 39.7 + - + -
217B HIS 3.6 1.9 - - - +
218B VAL* 3.5 2.2 - - - -
219B VAL* 2.9 32.8 + - + +
222B GLY* 5.5 2.2 - - - +
247B GLN* 4.4 1.9 + - - -
249B ASN* 4.9 3.8 - - - +
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Residues in contact with ASP 182 (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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147B VAL* 4.3 3.1 - - - +
181B GLN* 1.3 90.1 + - - +
183B PHE* 1.3 61.2 + - - +
184B TYR* 2.5 34.4 + - - -
215B PRO* 3.6 22.9 - - + -
217B HIS 3.5 5.4 - - - -
218B VAL* 4.1 9.2 - - + +
247B GLN* 2.9 26.6 + - - +
249B ASN* 3.0 26.9 + - - +
250B ARG* 3.6 6.8 - - + +
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Residues in contact with PHE 183 (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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50B ILE* 5.1 7.6 - - + -
52B ILE* 4.3 26.2 - - + -
59B VAL* 4.2 22.7 - - + -
68B VAL* 4.4 13.2 - - + -
147B VAL* 2.8 31.9 - - - -
148B SER* 3.8 15.3 - - - -
181B GLN* 3.1 33.0 - - + -
182B ASP* 1.3 72.0 - - - +
184B TYR* 1.3 75.8 + - - +
185B VAL* 4.0 15.9 - - + -
215B PRO* 3.1 19.2 - - - +
216B THR* 3.3 5.2 + - - -
217B HIS* 2.9 20.9 + - + +
219B VAL* 4.5 13.7 - - + -
222B GLY 4.6 5.4 - - - -
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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