Contacts of the helix formed by residues 102 - 116 (chain B) in PDB entry 1VLA
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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B VAL* 3.8 36.6 - - + -
66B GLN* 3.8 10.8 - - - +
97B PHE* 3.5 42.8 - - + -
100B GLU 3.5 0.9 - - - +
101B PRO* 1.4 78.5 - - + +
103B LYS* 1.3 60.0 + - - +
104B ASP* 3.4 2.5 - - - -
105B LYS* 3.2 12.0 + - + -
106B VAL* 3.0 26.8 + - + +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B GLU* 4.0 20.7 + - - +
101B PRO* 2.9 26.0 + - + +
102B PRO* 1.3 69.0 - - - +
104B ASP* 1.3 65.8 + - - +
106B VAL* 3.8 0.3 - - - +
107B GLU* 2.9 42.9 + - - +
136B TYR* 3.5 50.2 - - + +
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO 3.4 0.6 - - - -
103B LYS* 1.3 78.0 - - - +
105B LYS* 1.3 63.7 + - + +
107B GLU* 3.5 13.6 + - - +
108B LYS* 3.0 28.2 + - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 4.0 7.6 - - + -
61B MSE 2.7 62.4 + - + +
62B LYS 5.0 0.2 + - - -
63B VAL* 3.5 26.2 - - + +
102B PRO* 3.2 16.4 + - + +
104B ASP* 1.3 85.2 - - + +
106B VAL* 1.3 58.4 + - - +
108B LYS* 3.3 5.5 + - - +
109B ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 4.0 15.7 - - + -
95B PHE* 3.4 34.1 - - + -
97B PHE* 3.7 34.8 - - + -
102B PRO* 3.0 22.9 + - + +
103B LYS 3.8 0.2 - - - +
105B LYS* 1.3 72.7 - - - +
107B GLU* 1.3 60.8 + - - +
109B ALA* 3.2 2.2 + - - +
110B VAL* 2.9 30.3 + - - +
134B ILE* 3.9 9.9 - - + -
136B TYR* 3.2 25.1 - - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 2.9 39.7 + - - +
104B ASP* 3.7 12.3 + - - +
106B VAL* 1.3 75.4 - - - +
108B LYS* 1.3 53.4 + - - +
110B VAL* 4.0 0.3 - - - +
111B GLN* 2.7 39.7 + - - +
134B ILE* 3.8 23.8 - - + -
136B TYR* 5.1 2.6 - - + +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MSE 3.9 22.7 - - + -
104B ASP* 3.0 15.7 + - - +
105B LYS* 3.5 9.6 - - - +
106B VAL 3.2 0.2 - - - -
107B GLU* 1.3 75.3 - - - +
109B ALA* 1.3 53.6 + - - +
111B GLN* 3.7 22.6 + - - +
112B LEU* 2.8 63.8 + - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B VAL* 4.2 12.4 - - + +
57B ILE* 3.7 37.7 - - + +
58B LEU* 3.9 19.5 - - + -
105B LYS 2.9 17.3 + - - +
106B VAL* 3.4 5.4 - - - +
108B LYS* 1.3 75.5 - - - +
110B VAL* 1.3 63.5 + - - +
112B LEU* 3.5 2.4 + - - +
113B SER* 3.1 23.2 + - - -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B VAL* 3.8 23.6 - - + -
93B TYR* 3.8 35.9 - - + -
95B PHE* 4.2 14.4 - - + -
106B VAL 2.9 20.1 + - - +
107B GLU 4.0 2.5 - - - +
109B ALA* 1.3 73.5 - - - +
111B GLN* 1.3 59.4 + - - +
113B SER* 3.3 2.9 + - - -
114B GLN* 2.8 29.4 + - + +
132B TYR* 3.7 30.7 - - + -
134B ILE* 4.2 16.4 - - + -
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B GLU 2.7 22.2 + - - +
108B LYS* 3.7 29.9 + - - +
110B VAL* 1.3 73.6 - - - +
112B LEU* 1.3 54.1 + - + +
115B GLU* 2.7 58.0 + - + +
116B LYS 3.6 0.2 + - - -
132B TYR* 4.4 8.9 - - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 4.0 29.6 - - + -
61B MSE 5.5 1.6 - - + -
108B LYS* 2.8 60.0 + - + +
109B ALA 3.7 4.3 - - - +
111B GLN* 1.3 72.2 - - - +
113B SER* 1.3 61.0 + - - +
116B LYS* 2.9 47.9 + - + +
117B TYR* 2.8 40.3 + - + +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR* 2.6 31.9 + - - -
53B ASP* 2.6 36.1 + - - -
54B VAL* 4.4 3.8 - - - -
109B ALA 3.1 14.7 + - - -
110B VAL* 3.6 5.2 - - - -
112B LEU* 1.3 81.2 - - - +
114B GLN* 1.3 56.8 + - - +
117B TYR* 3.8 6.4 - - - -
118B CYS 3.0 7.3 + - - -
119B SER* 3.0 27.9 + - - -
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR* 4.5 0.4 + - - -
91B LEU* 3.3 26.1 - - - +
93B TYR* 2.9 31.9 + - + +
110B VAL 2.8 20.2 + - - +
111B GLN 4.1 0.2 - - - +
113B SER* 1.3 75.1 - - - +
115B GLU* 1.3 63.8 + - - +
118B CYS* 3.3 20.8 - - - +
119B SER 4.8 0.4 - - - +
120B VAL* 4.0 15.4 - - - +
121B SER* 3.9 11.1 + - - -
130B VAL* 4.4 12.4 - - - +
132B TYR* 3.5 50.6 - - + +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLN* 2.7 36.3 + - + +
114B GLN* 1.3 79.6 - - - +
116B LYS* 1.3 57.0 + - + +
118B CYS* 3.4 14.7 - - - -
129B LYS* 4.6 20.7 + - - -
132B TYR* 2.7 42.8 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A HIS* 3.8 14.6 - - + +
83A PRO* 3.8 23.6 - - - +
111B GLN 3.6 0.8 + - - -
112B LEU* 2.9 43.5 + - + +
115B GLU* 1.3 79.0 - - - +
117B TYR* 1.3 85.3 + - + +
118B CYS* 3.2 1.9 + - - -
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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