Contacts of the strand formed by residues 178 - 183 (chain A) in PDB entry 3HVJ
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 LEU 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.0 28.0 - - + -
106A LEU* 3.9 33.9 - - + +
130A LEU* 5.2 2.5 - - + -
169A LEU* 4.6 9.4 - - + -
175A VAL* 4.0 12.8 - - + -
177A THR* 1.3 76.2 - - - +
179A ASP* 1.3 56.1 + - - +
180A MET 4.2 10.5 - - - +
181A VAL* 3.8 25.6 - - + -
197A LEU* 3.9 14.8 - - + -
202A LEU* 2.8 26.6 + - + +
203A LEU* 4.6 1.6 - - + -
204A ARG* 3.9 5.0 - - - +
207A THR* 2.7 30.4 + - + +
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Residues in contact with ASP 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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100A TYR* 6.0 0.7 - - - +
102A PRO* 3.8 17.7 - - + +
103A SER* 3.2 15.0 + - - -
104A LEU* 2.8 37.7 + - - +
177A THR* 4.7 5.6 + - - +
178A LEU* 1.3 75.5 - - - +
180A MET* 1.3 61.5 + - - +
204A ARG* 3.0 34.2 + - - +
206A GLY 4.2 2.4 - - - +
207A THR* 3.5 6.6 - - - -
208A VAL* 3.0 23.0 + - - +
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Residues in contact with MET 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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93A MET* 5.2 0.9 - - + +
96A VAL* 4.0 29.4 - - + -
97A ILE* 3.6 37.5 - - + -
100A TYR* 5.7 2.2 - - + -
102A PRO* 4.0 20.0 - - + -
104A LEU 3.4 3.1 + - - +
105A VAL* 3.3 10.5 - - + -
106A LEU* 2.8 24.8 + - - +
119A MET* 4.2 16.2 - - - -
178A LEU* 3.5 2.7 - - - +
179A ASP* 1.3 81.8 - - - +
181A VAL* 1.3 73.8 + - - +
182A PHE* 4.9 3.6 - - + -
207A THR* 4.5 0.4 - - - -
208A VAL* 3.2 19.7 - - + +
210A LEU* 4.2 23.6 - - + -
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Residues in contact with VAL 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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106A LEU* 3.2 13.5 - - + +
108A LEU* 4.4 10.8 - - + -
178A LEU* 3.8 28.9 - - + -
180A MET* 1.3 82.8 - - - +
182A PHE* 1.3 60.2 + - - +
183A LEU* 4.0 20.2 - - + +
197A LEU* 4.1 21.8 - - + -
203A LEU* 4.4 3.4 - - + -
207A THR* 4.6 1.1 - - + -
208A VAL 2.8 7.3 + - - +
209A LEU* 3.4 24.2 - - + -
210A LEU* 2.8 32.7 + - - +
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Residues in contact with PHE 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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85A VAL* 4.3 8.3 - - + -
93A MET* 3.1 35.2 - - + -
105A VAL* 4.9 0.6 - - + +
106A LEU 2.8 11.3 + - - +
107A GLU* 3.4 18.0 - - + -
108A LEU* 2.9 28.2 + - - +
115A SER* 3.5 14.8 - - - -
119A MET* 3.9 25.1 - - + -
180A MET* 4.9 3.0 - - + +
181A VAL* 1.3 72.6 - - - +
183A LEU* 1.3 60.4 + - - +
184A ASP* 3.5 21.5 + - + -
210A LEU* 3.2 35.4 - - + -
212A ASP* 3.9 29.8 - - + -
250A LEU* 4.4 4.9 - - + -
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Residues in contact with LEU 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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108A LEU* 4.3 19.5 - - + -
181A VAL* 4.0 24.0 - - + +
182A PHE* 1.3 72.0 - - - +
184A ASP* 1.3 62.2 + - - +
185A HIS* 4.4 1.8 - - + -
190A TYR* 3.2 48.5 + - + +
193A ASP* 5.3 0.2 - - + -
194A THR* 3.8 22.7 - - - +
197A LEU* 5.8 1.3 - - + -
209A LEU* 4.0 22.7 - - + -
210A LEU 2.9 23.7 + - - +
211A ALA* 4.2 6.1 - - + -
212A ASP* 3.0 25.6 + - - +
222A PHE* 4.2 4.3 - - + -
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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