Contacts of the helix formed by residues 66 - 81 (chain A) in PDB entry 3V4R
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 ASN 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 3.2 5.6 + - - +
65A HIS* 1.4 105.1 + - - +
67A LYS* 1.3 57.6 + - - +
68A THR* 3.0 15.5 + - - +
69A LEU* 2.8 41.3 + - - +
70A ALA* 3.0 26.0 + - - +
141A SER* 5.5 3.1 - - - -
507A GLU* 5.8 3.8 - - - +
4D T 3.4 27.3 - - - +
5D G 3.4 8.5 - - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 1.3 68.4 - - - +
68A THR* 1.3 55.7 + - - +
70A ALA* 4.0 7.2 - - - -
71A GLY* 2.8 29.3 + - - -
88A TYR* 3.5 12.9 + - - +
90A VAL* 3.6 36.1 - - + -
91A SER* 4.1 12.1 + - - -
93A TYR 4.0 18.4 + - - -
119A ILE* 5.9 2.9 - - + +
141A SER* 4.9 1.8 - - - -
5D G 3.0 29.9 + - - +
6D T 3.0 32.7 + - - +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 3.0 11.3 + - - +
67A LYS* 1.3 76.3 - - - +
69A LEU* 1.3 64.5 + - + +
71A GLY* 3.3 3.3 + - - -
72A GLN* 3.2 31.0 + - - +
481A THR* 3.3 30.3 + - - +
484A ARG* 3.9 21.8 + - - +
507A GLU* 3.9 24.0 - - + -
5D G 4.1 3.8 + - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 4.2 15.7 - - + -
65A HIS* 3.8 32.8 - - + +
66A ASN* 2.8 24.8 + - - +
68A THR* 1.3 71.3 - - + +
70A ALA* 1.3 65.9 + - - +
72A GLN* 3.4 21.5 + - - +
73A LEU* 3.1 29.0 + - + +
338A ASP* 3.3 28.7 - - + +
339A GLU* 4.2 9.9 - - + -
507A GLU* 5.6 8.7 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 3.8 17.6 - - + +
66A ASN 3.0 17.7 + - - +
67A LYS* 3.6 10.3 - - - +
69A LEU* 1.3 72.4 - - - +
71A GLY* 1.3 64.8 + - - +
73A LEU* 3.1 2.7 + - - -
74A TYR* 3.0 22.3 + - - +
88A TYR* 3.8 16.6 - - + +
90A VAL* 4.6 8.3 - - + -
139A ILE* 3.4 19.5 - - + +
140A ALA 4.9 5.6 - - - +
141A SER* 5.4 0.9 - - - +
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS 2.8 17.4 + - - -
68A THR* 3.6 2.9 - - - -
69A LEU 3.3 0.2 - - - -
70A ALA* 1.3 76.9 - - - +
72A GLN* 1.4 59.4 - - - +
74A TYR* 3.3 6.0 + - - +
75A SER* 2.9 25.8 + - - -
88A TYR* 3.8 15.2 - - - -
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Residues in contact with GLN 72 (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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68A THR* 3.2 26.3 + - + +
69A LEU* 3.7 23.4 - - - +
70A ALA 3.3 0.2 - - - -
71A GLY* 1.4 73.4 - - - +
73A LEU* 1.4 58.1 + - + +
75A SER* 3.3 10.7 + - - -
76A GLU* 2.9 42.6 + - - +
484A ARG* 5.0 10.5 - - - +
507A GLU* 5.0 5.8 - - - +
508A GLY* 5.5 4.0 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.4 26.0 - - - +
62A VAL* 4.1 21.5 - - + -
64A ALA* 4.3 14.8 - - + -
69A LEU* 3.1 18.8 + - + +
70A ALA 3.5 6.7 - - - +
72A GLN* 1.4 72.3 - - + +
74A TYR* 1.4 55.7 + - - +
76A GLU* 3.4 10.3 + - - +
77A PHE* 2.8 55.0 + - + -
139A ILE* 3.8 10.5 - - + -
338A ASP* 4.0 33.2 - - + +
701A ADP 5.1 1.8 - - - +
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Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 3.0 12.0 + - - +
71A GLY* 3.4 10.5 - - - +
73A LEU* 1.4 72.2 - - - +
75A SER* 1.3 58.7 + - - +
77A PHE* 3.2 1.6 + - - +
78A LYS* 2.8 68.6 + - + +
86A VAL* 3.4 32.2 + - + +
87A GLU* 3.8 19.3 - - - -
88A TYR* 3.8 35.7 - + + -
122A LEU* 4.6 13.9 - - + +
139A ILE* 3.7 12.0 - - + +
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 2.9 16.5 + - - -
72A GLN* 3.4 9.3 + - - -
74A TYR* 1.3 84.0 - - - +
76A GLU* 1.3 63.1 + - - +
78A LYS* 3.3 5.5 + - - +
79A GLU* 3.1 23.9 + - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.8 17.9 - - + -
72A GLN* 2.9 35.6 + - - +
73A LEU* 3.5 18.4 - - - +
75A SER* 1.3 77.6 - - - +
77A PHE* 1.4 60.0 + - - +
79A GLU* 3.5 8.1 + - - +
80A PHE* 3.2 31.4 + - + -
701A ADP 2.9 46.0 + - - +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.9 21.1 - - + -
49A VAL* 3.8 20.2 - - + -
50A SER* 3.3 27.4 - - - -
53A ILE* 3.6 22.0 - - + -
62A VAL* 4.0 17.3 - - + -
73A LEU* 2.8 43.2 + - + +
74A TYR 4.0 2.5 - - - +
76A GLU* 1.4 70.8 - - - +
78A LYS* 1.4 60.1 + - - +
79A GLU 3.2 0.4 - - - -
80A PHE* 3.2 2.8 + - - -
81A PHE* 2.9 44.4 + + + -
86A VAL* 3.7 21.4 - - + +
137A ILE* 4.4 4.5 - - + -
139A ILE* 3.3 25.1 - - + -
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 2.8 55.6 + - + +
75A SER* 3.3 6.5 + - - +
77A PHE* 1.4 71.4 - - - +
79A GLU* 1.4 60.2 + - - +
81A PHE 4.5 2.9 - - - +
82A PRO* 3.6 29.7 - - + +
84A ASN 5.0 5.3 + - - -
85A ALA* 5.7 0.2 - - - +
86A VAL* 2.8 44.0 + - + +
87A GLU* 5.1 3.2 + - - -
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Residues in contact with GLU 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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8A VAL* 3.7 11.3 - - - +
11A TYR* 4.2 14.6 + - - -
75A SER 3.1 12.4 + - - +
76A GLU* 3.6 12.5 - - - +
77A PHE 3.2 0.4 - - - -
78A LYS* 1.4 77.3 - - - +
80A PHE* 1.3 66.6 + - + +
82A PRO* 3.7 12.6 - - - +
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Residues in contact with PHE 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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7A LEU* 3.4 29.7 - - + -
8A VAL 2.8 38.2 + - - -
9A SER* 4.2 4.3 - - - -
11A TYR* 3.9 21.1 - + - -
46A THR* 4.1 15.3 - - + -
47A PHE* 3.5 34.8 - + + -
50A SER* 3.4 20.9 - - - -
76A GLU* 3.2 23.5 + - + -
77A PHE* 3.2 7.4 + - - +
79A GLU* 1.3 85.3 - - + +
81A PHE* 1.4 66.4 + - + +
82A PRO* 3.5 4.0 - - - +
701A ADP 3.9 20.6 - - - -
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Residues in contact with PHE 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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5A PHE* 4.2 21.3 - + + -
6A GLU 3.6 19.5 - - - -
7A LEU* 3.7 23.6 - - + -
50A SER* 3.3 50.9 - - - -
53A ILE* 4.4 7.4 - - + -
54A LYS* 4.4 2.5 - - + -
77A PHE* 2.9 24.2 + + - +
78A LYS* 3.7 7.5 - - - +
80A PHE* 1.4 81.2 - - + +
82A PRO* 1.4 63.2 - - - +
83A ASN 3.3 3.3 + - - -
84A ASN* 3.6 24.8 + - + +
86A VAL* 3.7 22.1 - - + +
137A ILE* 3.5 26.0 - - + -
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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