Contacts of the helix formed by residues 55 - 64 (chain A) in PDB entry 2VQ5
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 SER 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 1.3 77.1 - - - +
56A ALA* 1.3 66.4 + - - +
57A ASP* 3.4 18.4 + - - +
58A ASP* 3.2 22.4 + - - +
59A ILE* 3.0 22.5 + - - +
149A GLY 5.5 0.4 - - - -
150A LYS 3.8 18.1 + - - -
151A ASP* 3.8 14.6 + - - +
152A SER 4.3 1.8 - - - +
153A CYS* 3.9 0.4 - - - -
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Residues in contact with ALA 56 (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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55A SER* 1.3 73.1 + - - +
57A ASP* 1.3 53.4 + - - +
59A ILE* 3.3 0.9 + - - -
60A TRP* 2.8 38.3 + - - +
120A ARG* 3.7 27.4 - - - +
145A VAL* 3.8 10.5 - - + +
147A PRO* 3.8 32.9 - - + +
152A SER 4.4 2.4 + - - -
153A CYS* 3.6 17.0 - - + +
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Residues in contact with ASP 57 (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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55A SER* 3.1 11.5 + - - +
56A ALA* 1.3 76.7 - - - +
58A ASP* 1.3 65.5 + - - +
60A TRP* 3.9 4.5 - - - +
61A THR* 2.9 35.7 + - + +
120A ARG* 2.5 34.0 + - - +
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Residues in contact with ASP 58 (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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54A ALA* 5.4 0.5 - - - +
55A SER* 3.2 26.2 + - - +
57A ASP* 1.3 80.1 - - - +
59A ILE* 1.3 63.6 + - - +
61A THR* 3.2 19.6 + - - +
62A VAL* 3.7 12.3 - - - +
191A VAL* 3.8 26.6 - - + +
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Residues in contact with ILE 59 (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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52A VAL* 4.3 4.5 - - + -
54A ALA* 4.1 13.0 - - + -
55A SER 3.0 15.4 + - - +
56A ALA 3.9 2.2 - - - +
58A ASP* 1.3 73.4 - - - +
60A TRP* 1.3 67.1 + - - +
62A VAL* 3.3 13.9 + - - +
63A TYR* 3.3 29.2 + - + -
145A VAL* 3.9 10.3 - - + -
153A CYS* 3.7 15.7 - - - -
155A ILE* 3.7 26.0 - - + -
187A ILE* 4.3 2.7 - - + -
188A SER* 4.1 26.9 - - - +
191A VAL* 3.9 29.2 - - + -
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Residues in contact with TRP 60 (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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56A ALA 2.8 21.8 + - - +
57A ASP* 3.9 4.3 - - - +
59A ILE* 1.3 74.6 - - - +
61A THR* 1.3 60.5 + - + +
63A TYR* 3.1 17.3 + + + -
64A SER* 2.8 52.4 + - - -
115A VAL* 4.0 9.6 - - + -
116A ASP 3.6 19.3 - - - -
117A ASN* 2.9 33.1 + - - +
120A ARG* 3.4 51.1 - - + -
121A LEU 3.4 27.6 - - - -
122A LYS* 3.8 16.8 - - + -
143A ILE* 4.6 3.1 - - + -
145A VAL* 4.0 12.5 - - + +
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Residues in contact with THR 61 (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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57A ASP* 2.9 27.1 + - + +
58A ASP* 3.2 15.6 + - - +
59A ILE 3.3 0.4 - - - -
60A TRP* 1.3 78.7 - - + +
62A VAL* 1.3 63.4 + - - +
64A SER* 3.7 8.2 + - - -
65A TRP* 3.2 22.9 + - - +
197A LYS* 4.1 28.2 - - + -
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Residues in contact with VAL 62 (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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58A ASP 3.7 14.8 - - - +
59A ILE 3.3 6.4 + - - +
60A TRP 3.2 0.4 - - - -
61A THR* 1.3 78.9 + - - +
63A TYR* 1.3 64.8 + - - +
65A TRP* 3.2 25.2 + - + +
68A LEU* 3.5 24.1 - - + +
187A ILE* 3.7 31.0 - - + -
190A LEU* 4.7 17.5 - - + -
191A VAL* 3.8 20.4 - - + -
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Residues in contact with TYR 63 (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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59A ILE* 3.3 39.3 + - + +
60A TRP* 3.1 22.8 + + + +
62A VAL* 1.3 80.4 - - - +
64A SER* 1.3 59.1 + - - +
65A TRP 3.6 1.7 + - - +
68A LEU* 4.1 7.3 - - + +
122A LYS* 3.2 36.1 + - + +
143A ILE* 3.8 30.3 - - + +
145A VAL* 4.2 7.0 - - + -
155A ILE* 3.6 18.5 - - + +
157A SER* 4.6 1.7 + - - -
180A LEU 4.7 0.3 + - - -
183A MSE 3.9 6.1 - - + +
184A ALA* 3.3 31.4 + - - +
187A ILE* 3.5 28.5 - - + -
1203A HBA 3.6 24.0 - - - -
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Residues in contact with SER 64 (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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60A TRP* 2.8 55.6 + - - -
61A THR* 3.7 9.9 + - - -
63A TYR* 1.3 72.0 - - - +
65A TRP* 1.3 62.7 + - - +
66A PRO* 3.3 10.9 - - - +
115A VAL* 4.0 18.4 - - - +
117A ASN* 3.9 9.1 + - - -
122A LYS* 5.8 0.2 - - - +
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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