Contacts of the strand formed by residues 175 - 184 (chain A) in PDB entry 6H2V
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 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 1.3 78.6 - - - +
176A ILE* 1.3 59.1 + - - +
207A PHE* 3.4 5.9 - - - -
208A SER* 2.8 45.3 + - - +
209A PHE 3.3 30.5 - - - +
210A HIS* 3.5 33.2 + - + +
211A HIS* 4.9 1.0 - - - -
302A SO4 3.4 21.0 + - - -
303A SO4 3.4 21.3 + - - +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A VAL* 3.8 16.8 - - + -
166A GLN* 4.0 27.4 - - + +
169A ALA* 3.8 26.5 - - + -
174A ILE 5.1 0.7 - - - +
175A LYS* 1.3 74.9 - - - +
177A ASP* 1.3 66.6 + - - +
178A ILE* 4.6 6.7 - - + -
205A ILE* 3.6 18.4 - - + -
206A ARG 3.6 4.9 - - - -
207A PHE* 3.6 24.0 - - + +
208A SER* 5.6 0.4 - - - -
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.0 30.7 + - - -
176A ILE* 1.3 79.5 - - - +
178A ILE* 1.4 70.6 + - - +
179A ILE* 3.2 12.3 + - - +
205A ILE* 3.4 4.4 - - - -
206A ARG* 2.8 48.2 + - + +
208A SER* 5.8 1.8 - - - +
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Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 4.2 36.1 - - + +
166A GLN* 4.8 10.3 - - + +
176A ILE* 4.6 12.3 - - + -
177A ASP* 1.4 76.5 + - - +
179A ILE* 1.3 64.3 + - - +
180A ALA 3.6 22.7 - - - +
181A GLU* 4.8 4.7 - - + +
203A ASP* 3.8 23.6 - - + +
204A LEU 3.8 3.6 - - - +
205A ILE* 3.7 30.5 - - + -
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 3.6 27.4 - - + -
47A TYR* 3.7 25.8 - - + +
154A TYR* 3.7 22.4 - - + -
177A ASP* 3.8 11.0 - - - +
178A ILE* 1.3 73.8 - - - +
180A ALA* 1.3 59.9 + - + +
204A LEU* 2.8 38.0 + - + +
206A ARG* 3.5 29.2 - - + +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A CYS* 5.6 5.8 - - - -
178A ILE* 3.5 8.0 - - - +
179A ILE* 1.3 83.1 - - + +
181A GLU* 1.3 62.2 + - - +
182A LEU* 4.0 19.7 - - + -
203A ASP* 3.5 4.3 - - - -
204A LEU* 2.8 38.0 + - + +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 4.6 2.9 - - - +
162A ARG* 3.2 26.5 + - - +
178A ILE* 4.8 4.0 - - + +
180A ALA* 1.3 74.1 - - - +
182A LEU* 1.3 63.1 + - - +
183A ARG* 3.2 38.8 + - - +
202A VAL 3.6 6.5 - - - +
203A ASP* 3.3 20.6 - - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.8 39.0 - - + +
38A CYS* 4.6 19.7 - - + -
39A MET* 5.7 1.8 - - + -
156A LEU* 3.7 29.8 - - + -
180A ALA* 4.3 19.5 - - + -
181A GLU* 1.3 74.9 - - - +
183A ARG* 1.3 65.8 + - - +
184A TYR* 4.1 3.4 - - + -
200A ILE 3.8 0.4 - - - +
201A GLU* 3.6 0.7 - - - -
202A VAL* 2.8 44.4 + - + +
204A LEU* 4.1 14.4 - - + -
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 5.1 5.1 - - - +
181A GLU* 3.2 52.3 + - - +
182A LEU* 1.3 76.8 - - - +
184A TYR* 1.3 59.9 + - - +
198A VAL* 3.8 19.1 - - + +
200A ILE 3.5 4.5 - - - -
201A GLU* 3.8 27.2 + - + +
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.5 37.6 + + - -
30A PRO 5.5 3.1 - - - -
31A THR* 6.1 0.4 - - - -
32A ARG* 4.5 17.0 - - + -
35A ILE* 3.9 43.3 - - + -
126A ASN* 3.6 15.7 + - - -
156A LEU* 4.3 4.3 - - + +
182A LEU* 4.7 2.0 - - + -
183A ARG* 1.3 75.4 - - - +
185A ASP* 1.3 67.2 + - - +
186A LEU* 5.4 1.1 - - - -
198A VAL* 3.6 6.3 - - - +
200A ILE* 2.9 70.7 + - + +
202A VAL* 3.7 31.1 - - + +
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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