Contacts of the helix formed by residues 161 - 171 (chain A) in PDB entry 2CVP
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ASN* 4.3 5.0 + - - +
156A GLY 3.4 19.6 - - - +
157A ILE* 3.8 7.0 - - - -
158A GLY 2.9 8.9 + - - +
159A GLY 3.2 0.4 - - - -
160A SER* 1.3 79.5 - - - +
162A LEU* 1.3 75.3 + - - +
163A GLY 3.4 2.0 - - - -
164A PRO* 3.4 4.6 - - - +
165A LEU* 3.0 41.0 + - - +
183A PHE* 3.7 25.3 - - - +
184A VAL 4.9 0.5 - - - +
185A SER* 3.5 26.6 + - - -
386B ASN* 4.1 6.2 + - - -
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Residues in contact with LEU 162 (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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158A GLY* 2.9 21.1 + - - +
159A GLY* 5.5 0.2 - - - -
161A ASP* 1.3 84.9 - - - +
163A GLY* 1.3 62.3 + - - +
165A LEU* 3.8 8.8 - - + +
166A MET* 2.8 33.6 + - - +
347A ARG* 5.4 6.7 - - + +
350A ALA* 3.7 29.6 - - + +
351A TYR* 3.8 14.5 - - + +
354A GLN* 3.5 37.0 - - + +
386B ASN* 6.0 3.4 - - + +
390B ALA* 4.3 13.5 - - + -
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Residues in contact with GLY 163 (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 GLY* 4.6 5.7 + - - -
162A LEU* 1.3 78.6 - - - +
164A PRO* 1.3 69.3 - - - +
166A MET* 3.8 0.7 - - - +
167A VAL* 2.9 28.9 + - - +
276A LEU* 3.8 16.4 - - - -
351A TYR* 3.3 27.6 - - - -
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Residues in contact with PRO 164 (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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154A ASN* 4.9 2.0 - - - +
159A GLY 4.4 2.0 - - - +
160A SER 4.1 8.5 - - - +
161A ASP 3.4 14.1 - - - +
163A GLY* 1.3 89.6 - - - +
165A LEU* 1.3 59.1 + - - +
168A THR* 2.9 32.9 + - - +
183A PHE* 3.6 9.9 - - + -
276A LEU* 4.5 3.1 - - + -
280A ILE* 3.5 38.8 - - + +
281A GLY* 4.9 1.8 - - - -
283A SER* 3.2 25.1 - - - +
284A ILE* 3.8 16.1 - - + +
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Residues in contact with LEU 165 (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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161A ASP* 3.0 39.1 + - - +
162A LEU* 3.8 9.6 - - + +
164A PRO* 1.3 76.8 - - - +
166A MET* 1.3 63.9 + - - +
168A THR* 3.1 3.4 + - - -
169A GLU* 3.0 37.9 + - + +
183A PHE* 3.6 34.0 - - + -
185A SER* 6.1 0.2 - - - +
346A HIS* 5.6 0.2 - - + -
347A ARG* 3.5 36.1 - - + +
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Residues in contact with MET 166 (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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162A LEU 2.8 21.7 + - - +
163A GLY 3.9 0.7 - - - +
165A LEU* 1.3 73.7 - - - +
167A VAL* 1.3 69.3 + - + +
169A GLU* 3.5 2.3 + - - +
170A ALA* 2.9 28.9 + - + +
344A TYR 4.7 0.7 - - - +
345A MET* 5.9 2.0 - - - -
347A ARG* 3.5 44.6 - - + +
348A PHE* 3.7 27.4 - - + +
351A TYR* 3.7 36.3 - - + -
487A LEU* 4.5 10.3 - - - -
491A ILE* 3.9 24.9 - - + -
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Residues in contact with VAL 167 (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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163A GLY 2.9 20.6 + - - +
166A MET* 1.3 81.3 - - - +
168A THR* 1.3 57.7 + - - +
170A ALA* 3.1 3.8 + - - -
171A LEU* 2.9 52.8 + - + +
276A LEU* 3.9 23.6 - - + -
284A ILE* 3.7 34.8 - - + -
296A LEU* 4.0 8.1 - - + -
487A LEU* 4.0 6.3 - - + -
491A ILE* 4.1 18.8 - - + -
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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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164A PRO 2.9 24.8 + - - +
165A LEU 3.1 7.8 + - - -
167A VAL* 1.3 75.7 - - - +
169A GLU* 1.3 63.2 + - - +
171A LEU* 3.7 3.6 - - - +
172A LYS* 3.2 30.0 + - - -
181A VAL* 4.0 7.3 - - + +
183A PHE* 3.3 24.6 - - + -
283A SER 4.1 7.9 - - - +
284A ILE* 3.8 29.8 - - + +
287A HIS* 3.7 24.2 - - + -
288A VAL* 5.4 2.7 - - + -
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Residues in contact with GLU 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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165A LEU* 3.0 37.5 + - + +
166A MET* 3.7 5.4 - - - +
168A THR* 1.3 78.6 + - - +
170A ALA* 1.3 61.9 + - - +
171A LEU 3.3 0.9 + - - -
172A LYS* 3.4 32.1 + - - +
181A VAL* 6.0 0.2 - - - +
183A PHE* 6.0 1.8 - - + -
344A TYR* 3.4 27.7 - - - +
346A HIS* 2.7 38.9 + - + +
347A ARG* 4.6 2.5 - - + -
194B LYS* 5.3 4.5 + - - -
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Residues in contact with ALA 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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166A MET* 2.9 23.0 + - - +
167A VAL 3.1 4.0 + - - +
169A GLU* 1.3 76.5 - - - +
171A LEU* 1.3 63.9 + - - +
172A LYS 3.4 1.0 + - - -
173A PRO* 4.2 3.5 - - - +
174A TYR* 5.5 0.5 - - - -
344A TYR* 3.3 32.1 + - - +
345A MET* 4.7 5.2 - - + -
413A GLN* 5.9 0.9 + - - +
482A LEU* 3.9 22.5 - - + +
487A LEU* 3.8 25.1 - - + -
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Residues in contact with LEU 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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167A VAL* 2.9 35.9 + - + +
168A THR 3.7 2.9 - - - -
170A ALA* 1.3 81.8 - - + +
172A LYS* 1.3 64.7 + - - +
173A PRO* 3.3 5.4 - - - -
174A TYR* 2.9 31.5 + - + +
284A ILE* 5.1 1.1 - - + -
288A VAL* 3.6 28.8 - - + +
292A HIS 5.3 0.4 - - - +
296A LEU* 4.6 5.4 - - + -
482A LEU* 4.3 6.5 - - + +
483A THR 4.0 5.8 - - - +
484A PRO* 3.8 44.4 - - + -
487A LEU* 3.7 22.0 - - + -
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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