Contacts of the helix formed by residues 152 - 162 (chain X) in PDB entry 1ZV4
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 ASP 152 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151X LEU* 1.3 76.5 - - - +
153X SER* 1.3 60.5 + - - +
154X ARG* 4.2 10.8 - - + +
155X VAL* 3.2 8.3 + - + +
156X ARG* 2.9 25.2 + - - +
177X GLN* 3.0 34.0 + - - +
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Residues in contact with SER 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X LEU 3.9 0.6 + - - -
152X ASP* 1.3 69.9 - - - +
154X ARG* 1.3 67.4 + - - +
156X ARG* 3.0 10.1 + - - +
157X GLU* 2.8 36.8 + - - +
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Residues in contact with ARG 154 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152X ASP* 4.2 8.5 - - + +
153X SER* 1.3 80.8 - - - +
155X VAL* 1.3 64.3 + - + +
157X GLU* 3.6 4.4 + - - +
158X VAL* 3.4 20.1 + - - +
161X ARG* 5.0 2.9 + - - -
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Residues in contact with VAL 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X LEU* 4.2 15.0 - - + -
152X ASP* 3.2 10.8 + - + +
153X SER 3.2 0.4 - - - -
154X ARG* 1.3 81.7 - - + +
156X ARG* 1.3 62.6 + - - +
158X VAL* 3.0 25.8 - - + +
159X ILE* 3.4 9.5 + - - +
173X ASP* 4.3 16.4 - - + +
174X ALA* 3.6 37.9 - - + +
177X GLN* 3.3 27.1 - - - +
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Residues in contact with ARG 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X TYR* 5.1 5.5 + - - -
141X ILE* 2.6 47.8 + - + +
143X ILE* 4.3 17.6 - - - +
148X GLU* 3.6 29.2 + - - +
149X VAL 4.6 3.2 + - - -
151X LEU* 4.1 32.7 + - + +
152X ASP 2.9 18.0 + - - +
153X SER* 3.0 11.4 + - - +
155X VAL* 1.3 77.8 - - - +
157X GLU* 1.3 66.0 + - - +
159X ILE* 3.2 11.6 + - + +
160X ASN* 3.0 38.2 + - - +
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Residues in contact with GLU 157 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X SER* 2.8 24.9 + - - +
154X ARG* 4.2 4.3 - - - +
156X ARG* 1.3 79.0 - - - +
158X VAL* 1.3 65.1 + - - +
160X ASN* 3.2 26.5 + - - +
161X ARG* 3.2 40.4 + - - +
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Residues in contact with VAL 158 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X ARG 3.4 8.1 + - - +
155X VAL* 3.0 37.0 - - + +
157X GLU* 1.3 75.8 - - - +
159X ILE* 1.3 65.2 + - + +
161X ARG* 3.3 22.8 + - - +
162X ASN* 3.1 44.3 + - - +
170X MET 5.5 2.2 - - - +
173X ASP* 4.6 24.5 - - + +
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Residues in contact with ILE 159 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X TYR* 4.3 4.5 - - + -
141X ILE* 4.0 22.2 - - + -
151X LEU* 4.0 16.8 - - + -
155X VAL* 3.4 15.0 - - + +
156X ARG* 3.2 10.2 + - - +
158X VAL* 1.3 81.4 - - + +
160X ASN* 1.3 61.5 + - - +
162X ASN* 3.3 10.9 + - - +
163X LEU* 3.2 31.5 + - + +
170X MET* 4.3 9.6 - - + +
171X TYR* 3.7 37.9 - - + -
174X ALA* 3.9 26.2 - - + +
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Residues in contact with ASN 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X TYR* 4.0 21.7 + - - -
141X ILE* 5.6 0.5 - - - +
156X ARG* 3.0 25.5 + - - +
157X GLU* 3.2 37.2 + - - +
158X VAL 3.3 0.4 - - - -
159X ILE* 1.3 76.9 - - - +
161X ARG* 1.3 60.6 + - + +
163X LEU* 3.1 33.3 + - + +
164X LEU* 4.4 1.7 + - - +
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Residues in contact with ARG 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X ARG 5.0 2.6 + - - -
157X GLU* 3.2 24.3 + - - +
158X VAL* 3.8 30.7 - - - +
159X ILE 3.3 0.2 - - - -
160X ASN* 1.3 71.6 - - + +
162X ASN* 1.3 66.8 + - - +
163X LEU 3.1 5.6 + - - -
164X LEU* 4.2 8.0 + - - +
165X ASP* 4.9 2.8 + - - +
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Residues in contact with ASN 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X VAL* 3.1 33.8 + - - +
159X ILE* 3.6 5.8 - - - +
160X ASN 3.3 0.2 - - - -
161X ARG* 1.3 79.3 - - - +
163X LEU* 1.3 59.7 + - - +
164X LEU 3.5 0.9 - - - -
165X ASP 3.2 25.3 - - - +
166X PRO* 3.4 7.3 - - - +
167X ASN* 4.9 8.7 - - - +
170X MET* 3.4 47.2 + - + +
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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