Contacts of the strand formed by residues 167 - 175 (chain A) in PDB entry 4H34
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.3 41.8 - - + +
126A LEU* 3.8 34.1 - - + -
127A THR* 5.3 8.7 - - + +
150A SER* 6.0 0.2 - - - -
151A VAL 3.4 2.5 - - - +
152A ARG* 3.7 29.8 - - + -
166A LYS* 1.3 75.3 - - - +
168A THR* 1.3 62.4 + - - +
169A HIS* 4.0 11.7 + - + -
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Residues in contact with THR 168 (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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149A LEU 3.4 2.4 - - - +
150A SER* 3.4 2.8 - - - -
151A VAL* 2.8 42.4 + - - +
153A THR* 4.4 4.0 - - - +
166A LYS* 4.3 13.9 + - - +
167A VAL* 1.3 74.4 - - - +
169A HIS* 1.3 72.0 + - - +
170A VAL* 4.7 3.0 - - + +
204A GLU* 3.4 38.2 + - - +
210A LEU* 3.7 24.6 - - + +
608A GOL 5.6 3.6 - - - -
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Residues in contact with HIS 169 (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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119A GLY* 4.3 4.4 + - - -
122A ALA* 5.6 0.2 - - - +
123A GLU* 3.2 45.5 + - + +
138A ARG* 3.3 21.4 + - - -
148A VAL* 4.1 10.5 - - + -
149A LEU 3.4 4.5 - - - -
150A SER* 3.2 29.8 + - - -
167A VAL* 4.0 15.0 + - + +
168A THR* 1.3 76.5 - - - +
170A VAL* 1.3 61.7 + - - +
608A GOL 3.0 30.0 + - - +
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Residues in contact with VAL 170 (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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148A VAL* 4.3 2.7 - - - -
149A LEU* 2.7 58.0 + - + +
151A VAL* 5.6 1.8 - - + -
168A THR* 4.7 7.4 - - + +
169A HIS* 1.3 76.2 - - - +
171A MET* 1.3 72.7 + - - +
172A ILE* 3.8 0.5 + - - +
181A VAL* 3.9 18.2 - - + +
202A MET* 3.9 24.2 - - + -
204A GLU* 5.8 0.2 - - - +
210A LEU* 3.9 28.3 - - + -
608A GOL 4.4 13.5 - - - +
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Residues in contact with MET 171 (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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140A SER* 3.2 16.4 - - - +
142A SER* 5.1 1.3 - - - +
143A HIS* 3.2 39.3 - - + +
146A ASP* 4.5 12.3 - - - +
147A PHE 3.5 11.2 - - - +
148A VAL* 3.5 26.7 - - + +
169A HIS 4.2 1.4 + - - -
170A VAL* 1.3 75.5 - - - +
172A ILE* 1.3 61.4 + - - +
173A ARG* 4.0 10.1 - - + +
180A ASP 3.9 0.2 - - - +
181A VAL* 3.4 29.1 + - - +
608A GOL 4.4 9.8 + - - +
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Residues in contact with ILE 172 (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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137A VAL* 4.3 14.1 - - + -
146A ASP* 3.4 3.8 - - - +
147A PHE* 2.7 45.5 + - + +
148A VAL 4.3 1.6 - - - -
149A LEU* 3.8 29.8 - - + +
170A VAL 4.1 3.4 - - - +
171A MET* 1.3 75.3 - - - +
173A ARG* 1.3 60.5 + - - +
174A CYS 3.7 0.2 + - - -
179A TYR* 3.8 32.1 - - + -
180A ASP 3.4 4.0 - - - +
181A VAL* 4.3 7.0 - - + -
190A LEU* 3.9 24.7 - - + -
193A LEU* 3.8 33.2 - - + -
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Residues in contact with ARG 173 (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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146A ASP* 3.5 20.2 + - + +
171A MET* 4.0 12.7 - - + +
172A ILE* 1.3 72.3 - - - +
174A CYS* 1.3 60.3 + - - +
175A GLN* 3.7 36.9 + - + +
178A LYS 3.5 1.4 - - - +
179A TYR* 3.6 1.6 - - - -
180A ASP* 2.8 52.9 + - - +
181A VAL 5.4 0.4 - - - -
182A GLY* 5.5 7.4 - - - +
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Residues in contact with CYS 174 (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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145A GLY* 3.4 25.1 - - - +
146A ASP* 2.8 14.8 + - - +
172A ILE 3.7 1.4 + - - -
173A ARG* 1.3 68.8 - - - +
175A GLN* 1.3 62.2 + - - +
176A GLU 4.1 1.2 + - - -
177A LEU* 4.1 29.4 - - - -
178A LYS 3.5 3.8 - - - -
179A TYR* 3.6 31.9 - - + -
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Residues in contact with GLN 175 (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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173A ARG* 3.6 44.5 + - + +
174A CYS* 1.3 73.4 - - - +
176A GLU* 1.4 73.4 + - - +
177A LEU 3.6 0.2 - - - -
178A LYS 2.9 11.9 + - - -
180A ASP* 3.1 33.7 + - - +
182A GLY* 5.9 0.2 - - - -
186A ARG* 2.7 36.9 + - - +
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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