Contacts of the helix formed by residues 56 - 71 (chain A) in PDB entry 1VRR
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A CYS 2.8 18.5 + - - -
41A THR* 3.6 19.4 + - - -
42A LYS* 4.1 13.8 - - - +
54A LEU 3.7 1.0 + - - -
55A TYR* 1.3 71.6 - - - +
57A PRO* 1.3 62.9 - - - +
58A VAL* 3.1 22.5 + - - +
59A ALA* 3.1 11.8 + - - +
60A LEU* 2.8 33.6 + - - +
8D T 4.5 1.7 + - - -
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Residues in contact with PRO 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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42A LYS* 5.2 2.9 - - + -
55A TYR 3.7 7.6 - - - +
56A SER* 1.3 84.0 - - - +
58A VAL* 1.3 57.6 + - - +
60A LEU* 3.9 6.9 - - + +
61A ASN* 2.8 36.0 + - - +
131A PHE* 3.9 22.9 - - + +
170A MET* 4.3 11.6 - - + -
171A SER* 6.2 3.1 - - - +
174A ILE* 5.0 7.2 - - + -
7D A 3.5 35.4 - - + +
8D T 3.3 25.1 - - - +
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Residues in contact with VAL 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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56A SER* 3.3 8.1 - - - +
57A PRO* 1.3 78.9 - - - +
59A ALA* 1.3 61.6 + - - +
61A ASN* 3.7 3.4 - - - +
62A GLU* 3.1 37.9 + - + +
7D A 3.8 28.3 - - - +
8D T 3.9 21.3 - - - +
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Residues in contact with ALA 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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38A ALA 5.3 0.4 - - - +
39A CYS* 3.6 32.6 - - + +
41A THR* 4.7 6.1 - - + +
56A SER* 3.1 17.2 + - - +
58A VAL* 1.3 78.3 - - - +
60A LEU* 1.3 60.4 + - - +
62A GLU* 3.1 13.4 + - - +
63A ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 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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1A MET* 4.0 34.1 - - + -
34A ILE* 4.7 3.4 - - + -
36A ALA* 4.3 7.9 - - + +
39A CYS* 3.8 27.3 - - + -
55A TYR* 4.2 11.2 - - + -
56A SER 2.8 16.2 + - - +
57A PRO 3.9 3.4 - - - +
59A ALA* 1.3 76.8 - - - +
61A ASN* 1.3 60.4 + - - +
63A ALA* 3.5 2.9 + - - +
64A PHE* 2.9 33.0 + - + -
131A PHE* 3.9 25.4 - - + -
166A LEU* 5.1 2.5 - - + -
170A MET* 3.2 35.4 - - + -
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Residues in contact with ASN 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 PRO 2.8 21.8 + - - +
58A VAL* 3.7 4.9 - - - +
60A LEU* 1.3 76.3 - - - +
62A GLU* 1.3 60.0 + - - +
64A PHE* 3.1 4.1 + - - +
65A LYS* 2.8 32.0 + - - +
120A PHE* 5.4 3.7 - - - -
129A VAL* 3.9 36.2 + - - +
131A PHE* 4.4 8.6 + - - +
6D G 4.1 6.2 - - - +
7D A 3.0 24.4 + - - +
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Residues in contact with GLU 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 VAL* 3.1 28.8 + - + +
59A ALA* 3.5 11.8 - - - +
61A ASN* 1.3 75.9 - - - +
63A ALA* 1.3 63.2 + - - +
65A LYS* 3.8 8.9 - - + +
66A GLU* 3.1 28.1 + - - +
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Residues in contact with ALA 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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34A ILE* 3.7 31.9 - - + -
39A CYS* 4.4 7.0 - - - -
59A ALA 2.9 16.8 + - - +
60A LEU* 3.6 8.3 - - - +
62A GLU* 1.3 76.8 - - - +
64A PHE* 1.3 55.8 + - - +
66A GLU* 4.0 4.4 - - - +
67A LYS* 2.8 39.1 + - - +
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Residues in contact with PHE 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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1A MET* 4.5 9.2 - - - -
30A ILE* 4.7 7.6 - - + -
31A ILE* 4.4 20.6 - - + -
34A ILE* 3.6 25.6 - - + -
60A LEU* 2.9 25.6 + - + +
61A ASN* 3.1 9.3 + - - +
63A ALA* 1.3 78.6 - - - +
65A LYS* 1.3 59.6 + - - +
67A LYS* 3.5 1.8 + - - +
68A LEU* 2.8 48.1 + - + +
120A PHE* 4.4 1.6 - - + -
129A VAL* 3.8 42.2 - - + -
131A PHE* 4.3 6.5 - + - -
160A ILE* 4.1 21.1 - - + -
201A ILE* 3.8 29.2 - - + -
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Residues in contact with LYS 65 (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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61A ASN 2.8 20.4 + - - +
62A GLU* 3.8 9.4 - - + +
64A PHE* 1.3 69.7 - - - +
66A GLU* 1.3 68.6 + - - +
69A GLU* 2.7 61.2 + - + +
75A GLU* 5.9 2.2 + - - +
119A ASP* 4.2 26.9 + - - +
120A PHE* 3.8 17.9 - - + -
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Residues in contact with GLU 66 (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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62A GLU 3.1 15.5 + - - +
63A ALA* 4.0 5.1 - - - +
65A LYS* 1.3 80.2 - - - +
67A LYS* 1.3 79.1 + - - +
69A GLU* 4.1 7.1 - - - +
70A ALA* 3.1 23.8 + - + +
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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
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30A ILE* 3.7 23.5 - - + +
33A SER* 3.5 34.7 + - - +
34A ILE* 4.3 18.4 - - + +
63A ALA* 2.8 28.4 + - - +
64A PHE 3.8 1.3 - - - +
65A LYS 3.2 0.6 - - - -
66A GLU* 1.3 89.9 - - + +
68A LEU* 1.3 63.7 + - - +
70A ALA* 3.3 18.9 - - - +
71A LYS* 3.3 13.5 + - - +
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Residues in contact with LEU 68 (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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27A ILE* 5.6 1.3 - - + -
30A ILE* 3.5 26.2 - - + -
64A PHE* 2.8 39.4 + - + +
67A LYS* 1.3 70.5 - - - +
69A GLU* 1.3 65.9 + - - +
71A LYS 2.9 10.4 + - - -
73A TRP* 3.1 51.2 + - + +
120A PHE* 3.8 43.7 - - + -
127A ILE* 4.0 26.0 - - + -
129A VAL* 4.6 0.4 - - + -
160A ILE* 5.9 0.4 - - + -
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Residues in contact with GLU 69 (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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65A LYS* 2.7 64.9 + - + +
66A GLU* 4.1 5.8 + - - +
68A LEU* 1.3 71.9 - - - +
70A ALA* 1.3 58.2 + - - +
71A LYS 3.0 0.2 - - - -
72A GLY* 2.8 22.5 + - - -
73A TRP 3.5 19.9 - - - +
74A LYS* 5.7 0.7 - - - -
119A ASP 5.6 1.5 - - - +
120A PHE* 4.7 6.4 - - + -
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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
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66A GLU* 3.1 21.6 + - + +
67A LYS* 3.3 11.0 - - - +
68A LEU 3.2 0.2 - - - -
69A GLU* 1.3 76.8 - - - +
71A LYS* 1.3 62.2 + - + +
72A GLY 3.3 1.0 + - - -
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Residues in contact with LYS 71 (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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26A GLU* 3.3 40.8 + - - +
29A GLU* 4.8 13.5 + - - -
30A ILE* 4.0 17.0 - - + -
67A LYS 3.3 12.0 + - - +
68A LEU 2.9 11.1 + - - +
70A ALA* 1.3 80.7 - - + +
72A GLY* 1.3 55.1 + - - +
73A TRP* 3.5 5.4 - - + -
122A LYS* 2.7 26.7 + - - -
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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