Contacts of the helix formed by residues 73 - 86 (chain A) in PDB entry 3VJR
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 LEU 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR* 3.3 23.7 + - + +
70A PHE* 2.9 18.9 + - + +
72A ASN* 1.3 95.1 - - - +
74A SER* 1.3 63.8 + - - +
76A LYS* 3.1 43.0 + - + +
122A ASP* 3.1 9.9 - - - +
126A LYS* 4.0 25.1 - - - +
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Residues in contact with SER 74 (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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12A LEU* 3.8 21.8 - - - +
13A ALA 4.7 2.3 + - - -
67A PRO* 4.3 9.9 - - - +
69A THR* 3.6 9.1 + - - -
70A PHE 3.5 1.5 + - - -
71A MET* 2.8 37.5 + - - -
73A LEU* 1.3 77.1 - - - +
75A GLY* 1.3 62.8 + - - +
77A ALA* 3.0 15.4 + - - +
78A VAL* 3.1 14.2 + - - +
119A GLY* 4.0 14.1 - - - -
122A ASP* 3.4 1.8 + - - -
123A ILE* 4.0 4.3 - - - -
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Residues in contact with GLY 75 (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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74A SER* 1.3 78.9 - - - +
76A LYS* 1.3 54.1 + - - +
78A VAL* 4.4 2.5 - - - -
79A ALA* 2.7 37.9 + - - +
122A ASP* 2.9 29.2 + - - -
123A ILE* 3.8 16.2 - - - +
126A LYS* 3.8 10.5 - - - -
127A LEU* 5.6 0.4 - - - +
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Residues in contact with LYS 76 (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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49A PHE* 3.7 43.4 - - + -
69A THR* 4.8 6.5 - - + -
73A LEU* 3.1 35.9 + - + +
75A GLY* 1.3 75.8 - - - +
77A ALA* 1.3 56.9 + - - +
79A ALA* 4.4 2.4 - - - +
80A ALA* 3.2 28.9 + - - +
126A LYS* 3.6 23.6 - - + +
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Residues in contact with ALA 77 (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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48A PHE 3.3 26.2 - - - +
49A PHE* 3.6 19.8 - - + +
65A LEU* 3.6 14.9 - - + +
67A PRO* 3.7 21.5 - - + -
69A THR* 4.8 1.8 - - + -
73A LEU 4.0 0.8 + - - -
74A SER 3.0 10.0 + - - +
76A LYS* 1.3 77.2 - - - +
78A VAL* 1.3 65.0 + - - +
80A ALA* 3.4 0.9 + - - +
81A MET* 3.2 18.7 + - - +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.3 6.9 - - + +
10A VAL* 3.9 33.2 - - + -
65A LEU* 4.1 6.3 - - + -
67A PRO* 5.4 0.7 - - + -
74A SER 3.1 15.8 + - - +
75A GLY* 3.9 4.9 - - - +
77A ALA* 1.3 75.8 - - + +
79A ALA* 1.3 57.4 + - - +
80A ALA 3.3 0.2 + - - -
81A MET* 3.4 1.9 + - - +
82A ALA* 2.9 28.8 + - - +
92A ILE* 4.1 20.6 - - + -
94A VAL* 5.3 0.9 - - + -
123A ILE* 3.9 33.9 - - + -
127A LEU* 3.9 20.9 - - + -
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Residues in contact with ALA 79 (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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75A GLY 2.7 22.8 + - - +
76A LYS* 4.4 3.6 - - - +
78A VAL* 1.3 73.4 - - - +
80A ALA* 1.3 57.0 + - - +
82A ALA* 4.1 1.3 - - - +
83A SER* 3.0 34.9 + - - +
126A LYS* 3.5 29.8 - - + +
127A LEU* 4.2 10.5 - - + +
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Residues in contact with ALA 80 (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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47A LYS 3.9 21.8 - - - +
48A PHE* 3.9 9.7 - - + -
49A PHE* 4.3 8.1 - - + -
76A LYS 3.2 21.3 + - - +
77A ALA 3.9 3.4 - - - +
78A VAL 3.2 0.2 - - - -
79A ALA* 1.3 75.6 - - - +
81A MET* 1.3 59.4 + - - +
83A SER* 3.9 3.2 - - - -
84A PHE* 3.0 30.3 + - - +
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Residues in contact with MET 81 (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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8A LEU* 4.0 16.6 - - + -
48A PHE* 3.5 32.3 - - + -
52A THR* 3.4 35.0 - - + -
63A ARG* 3.8 27.6 - - + +
64A LEU 4.8 0.4 - - - +
65A LEU* 3.8 22.7 - - + -
77A ALA 3.2 16.5 + - - +
78A VAL 4.0 2.0 - - - +
80A ALA* 1.3 72.5 - - - +
82A ALA* 1.3 67.5 + - - +
84A PHE 3.4 0.2 + - - -
85A PHE* 3.0 58.0 + - + +
87A ILE* 5.1 1.3 - - - -
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Residues in contact with ALA 82 (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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8A LEU* 4.5 2.8 - - + +
78A VAL 2.9 19.9 + - - +
79A ALA* 4.1 4.9 - - - +
81A MET* 1.3 75.5 - - - +
83A SER* 1.3 59.3 + - - +
85A PHE 3.4 0.2 + - - -
86A ARG* 2.8 10.4 + - - -
87A ILE* 2.8 55.1 + - + +
92A ILE* 4.2 20.0 - - + -
127A LEU* 4.6 6.3 - - + -
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Residues in contact with SER 83 (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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79A ALA* 3.0 21.5 + - - +
80A ALA* 3.9 4.5 - - - -
82A ALA* 1.3 74.4 - - - +
84A PHE* 1.3 66.3 + - - +
86A ARG* 3.3 15.8 + - - +
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Residues in contact with PHE 84 (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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47A LYS* 4.2 22.2 - - + -
48A PHE* 3.4 32.5 - + + -
80A ALA 3.0 19.3 + - - +
81A MET 3.4 2.0 + - - +
83A SER* 1.3 76.6 - - - +
85A PHE* 1.3 89.7 + + - +
86A ARG* 3.5 18.2 + - - -
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Residues in contact with PHE 85 (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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7A LYS* 5.4 2.3 + - - +
48A PHE* 4.0 11.9 - + - -
63A ARG* 3.4 56.5 - - - -
81A MET* 3.0 45.5 + - + +
84A PHE* 1.3 108.2 - + - +
86A ARG* 1.3 82.5 + - - +
87A ILE* 3.3 23.4 + - + +
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Residues in contact with ARG 86 (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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7A LYS* 4.3 12.3 + - - -
82A ALA 2.8 8.0 + - - -
83A SER* 3.3 11.9 + - - +
84A PHE 3.5 17.7 + - - +
85A PHE* 1.3 91.3 + - - +
87A ILE* 1.3 57.2 + - - +
88A ASN* 4.0 5.9 + - - +
91A GLU* 4.6 0.5 - - - +
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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