Contacts of the helix formed by residues 104 - 111 (chain A) in PDB entry 1VEP
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 PRO 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A TRP* 3.6 45.8 - - + +
53A GLY* 3.9 8.5 - - - +
56A GLU 3.3 18.8 - - - +
57A LYS* 4.6 5.6 - - + +
102A PRO 3.8 0.4 - - - -
103A ILE* 1.3 86.9 - - + +
105A SER* 1.3 65.5 + - - +
106A TRP* 3.1 32.7 + - + +
107A VAL* 3.0 28.2 - - + +
108A TRP* 4.0 1.2 - - - -
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Residues in contact with SER 105 (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 LYS 5.1 2.9 + - - -
103A ILE 3.2 4.2 + - - -
104A PRO* 1.3 73.1 - - - +
106A TRP* 1.3 68.4 + - - +
107A VAL 3.3 0.5 + - - -
108A TRP* 3.3 29.7 + - - +
109A ASN* 4.2 6.3 + - - -
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Residues in contact with TRP 106 (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 TRP* 4.6 5.8 - + - -
56A GLU* 3.0 50.9 + - + -
57A LYS 3.5 15.7 - - - -
58A ASN 4.0 3.4 - - - +
59A GLY* 3.5 20.1 - - - -
60A ASP* 3.5 34.5 - - + -
104A PRO* 3.1 18.4 - - + +
105A SER* 1.3 78.6 + - - +
107A VAL* 1.3 87.9 + - + +
108A TRP 3.1 2.7 - - - -
109A ASN* 3.0 31.6 + - - +
110A GLN* 3.9 20.1 + - + +
141A GLU* 3.3 25.6 - - - -
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Residues in contact with VAL 107 (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 TRP* 4.0 25.6 - - + -
103A ILE* 4.0 23.6 - - + -
104A PRO* 3.0 22.8 + - + +
106A TRP* 1.3 97.3 - - + +
108A TRP* 1.3 75.4 + - + +
109A ASN 3.3 0.7 + - - -
110A GLN* 3.3 22.2 + - - +
116A LEU* 3.4 11.1 - - + +
130A LEU* 4.2 17.9 - - + -
137A VAL* 4.6 2.0 - - + -
141A GLU* 4.3 13.9 - - + -
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Residues in contact with TRP 108 (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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103A ILE* 3.4 29.1 + - + +
104A PRO 4.0 2.1 + - - -
105A SER* 3.3 31.5 - - - +
106A TRP 3.1 1.0 - - - -
107A VAL* 1.3 79.4 - - + +
109A ASN* 1.3 63.9 + - - +
110A GLN 3.2 1.8 + - - -
111A LYS 3.6 12.3 - - - +
116A LEU* 3.6 52.4 - - + +
117A TYR* 4.0 10.8 - + + -
127A LYS* 3.3 71.4 - - + +
129A THR 4.3 4.0 - - - -
130A LEU* 4.0 15.3 - - + -
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Residues in contact with ASN 109 (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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105A SER 4.2 4.1 + - - +
106A TRP* 3.0 28.1 + - - +
108A TRP* 1.3 79.2 - - - +
110A GLN* 1.3 59.5 + - - +
111A LYS 3.1 11.9 + - - +
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Residues in contact with GLN 110 (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 ASP* 4.7 1.6 - - - +
106A TRP* 3.9 17.9 - - + +
107A VAL* 3.5 18.1 + - - +
108A TRP 3.2 1.8 - - - -
109A ASN* 1.3 78.2 - - - +
111A LYS* 1.3 73.5 + - + +
116A LEU* 4.7 1.1 - - + -
137A VAL* 3.3 36.7 - - + +
140A LYS* 4.0 11.9 + - - +
141A GLU* 2.8 29.0 + - - +
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Residues in contact with LYS 111 (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 TRP 3.6 13.0 + - - +
109A ASN* 3.1 6.6 - - - +
110A GLN* 1.3 87.7 - - - +
112A SER* 1.3 64.3 + - - +
113A ASP* 3.5 25.7 + - - +
115A SER* 3.6 12.1 - - - +
116A LEU* 3.2 33.8 - - + +
134A ALA* 5.6 0.7 - - - -
136A ASP* 2.9 26.0 + - - -
137A VAL* 3.5 23.8 - - + -
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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