Contacts of the strand formed by residues 174 - 183 (chain L) in PDB entry 2A6H
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 174 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44L LEU* 3.0 26.7 - - + +
45L LEU* 4.1 6.2 - - + +
48L ILE* 3.9 26.7 - - + -
172L SER* 2.5 30.2 + - - +
173L PRO* 1.3 80.1 - - + +
175L ARG* 1.3 63.1 + - - +
176L ARG 4.1 6.5 - - - +
177L VAL* 4.1 16.4 - - + -
199L ILE* 3.8 16.2 - - + -
200L TRP 3.4 16.2 - - - +
201L THR* 3.9 9.6 - - + -
210L ALA* 4.4 5.4 - - + -
851N LEU* 4.0 8.5 - - - +
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Residues in contact with ARG 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LEU* 5.0 0.2 - - - -
83L LYS 4.7 8.1 + - - -
84L GLU* 3.4 28.3 + - - -
86L VAL* 6.0 0.8 - - - +
170L VAL* 4.7 13.9 - - - +
172L SER 5.5 3.6 + - - -
173L PRO 3.6 0.4 + - - -
174L VAL* 1.3 73.3 - - - +
176L ARG* 1.3 61.3 + - - +
200L TRP* 2.8 22.4 + - + +
201L THR 4.1 5.6 - - - +
202L ASP* 3.5 44.6 - - - +
845N ASN* 4.1 18.4 - - - +
847N ASP* 4.3 30.8 + - - +
848N GLU* 4.4 18.8 + - - +
851N LEU* 2.9 38.4 - - - +
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Residues in contact with ARG 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ARG* 6.1 0.7 - - - +
45L LEU* 4.6 4.7 - - - -
174L VAL* 3.7 2.4 - - - +
175L ARG* 1.3 85.0 - - + +
177L VAL* 1.3 73.0 + - - +
178L ALA* 5.0 7.9 - - - +
199L ILE* 3.7 1.7 - - - -
200L TRP* 3.0 75.6 + - + +
847N ASP* 4.9 11.6 + - + +
850N LEU* 6.6 0.2 - - + -
851N LEU* 4.9 3.1 - - + -
881N LEU* 5.7 0.6 - - - +
884N ARG* 2.8 46.5 - - - +
888N GLU* 2.8 40.2 + - - -
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Residues in contact with VAL 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ARG* 2.7 67.5 + - + +
44L LEU* 3.4 42.2 - - + -
45L LEU* 3.3 20.0 - - + -
174L VAL* 4.1 9.6 - - + -
176L ARG* 1.3 86.4 + - - +
178L ALA* 1.3 63.2 + - - +
179L PHE* 6.2 0.2 - - + -
197L LEU* 6.0 1.6 - - + -
198L ARG 3.4 3.6 - - - -
199L ILE* 4.2 9.2 - - + -
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Residues in contact with ALA 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ARG* 3.7 5.8 - - - +
176L ARG* 5.0 8.7 - - - +
177L VAL* 1.3 80.0 - - - +
179L PHE* 1.3 59.8 + - - +
196L THR 4.0 0.3 - - - +
197L LEU* 3.0 4.5 - - - +
198L ARG* 2.6 67.9 + - + +
200L TRP* 4.7 9.0 - - + -
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Residues in contact with PHE 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L GLY 5.0 0.7 - - - -
34L VAL* 4.8 17.3 - - + -
37L GLY* 3.7 15.9 - - - -
38L ASN* 3.7 36.8 - - + -
41L ARG* 4.1 27.1 - - + +
177L VAL* 6.2 0.2 - - + -
178L ALA* 1.3 78.1 - - - +
180L GLN* 1.3 67.9 + - - +
181L VAL* 4.8 11.8 - - + +
195L LEU* 4.0 17.0 - - + -
196L THR 3.3 4.9 - - - +
197L LEU* 3.6 18.4 - - + -
198L ARG* 5.5 2.0 - - - +
936N TYR* 4.7 6.9 + - - -
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Residues in contact with GLN 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179L PHE* 1.3 77.8 - - - +
181L VAL* 1.3 65.4 + - - +
182L GLU* 3.8 24.5 - - + +
194L LYS 3.2 2.8 - - - +
195L LEU* 3.7 3.6 - - - +
196L THR* 2.9 46.2 + - + +
198L ARG* 4.5 23.4 + - - +
636N GLN* 5.9 1.4 + - - -
936N TYR* 4.0 36.7 + - + +
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Residues in contact with VAL 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L GLY* 3.5 39.3 - - - +
34L VAL* 3.7 22.2 - - + +
179L PHE* 4.8 11.0 - - + +
180L GLN* 1.3 79.2 - - - +
182L GLU* 1.3 62.8 + - - +
183L ASP* 4.1 4.0 + - - +
193L ASP* 4.0 15.4 - - - +
194L LYS 3.2 13.0 - - - +
195L LEU* 4.5 2.5 - - + -
636N GLN* 4.7 9.5 + - - +
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Residues in contact with GLU 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L GLN* 4.1 28.4 - - + +
181L VAL* 1.3 74.4 - - - +
183L ASP* 1.3 71.7 + - - +
192L LEU 4.4 0.2 - - - -
193L ASP* 5.3 0.2 - - - -
194L LYS* 3.0 51.2 + - + +
196L THR* 4.2 15.0 - - + +
636N GLN* 5.7 2.2 - - - +
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Residues in contact with ASP 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181L VAL 4.7 2.4 - - - +
182L GLU* 1.3 83.8 - - - +
184L THR* 1.3 61.2 + - - +
190L THR 5.0 5.8 - - - +
191L ASP* 5.9 2.5 - - - -
192L LEU 3.3 16.5 + - - +
193L ASP* 5.5 1.2 - - - +
194L LYS* 5.1 1.6 - - - +
636N GLN* 4.4 17.6 + - - +
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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