Contacts of the helix formed by residues 52 - 66 (chain B) in PDB entry 1R1V
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ASN* 2.7 47.2 + - - -
51A LEU* 4.3 1.8 - - - -
52A SER* 4.4 5.2 - - - +
504A ZN 3.2 10.8 - - - -
46B SER* 4.2 0.9 - - - -
51B LEU* 1.3 74.5 - - - +
53B GLN* 1.3 64.7 + - - +
54B SER 3.8 2.6 + - - -
55B ASN* 3.1 22.2 + - - +
56B VAL* 3.0 20.6 + - - +
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Residues in contact with GLN 53 (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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42B VAL* 3.6 18.0 - - + +
43B GLY* 4.5 13.9 - - - +
46B SER* 3.6 25.3 + - - +
51B LEU 3.5 1.0 + - - -
52B SER* 1.3 71.7 - - - +
54B SER* 1.3 58.1 + - - +
56B VAL* 3.2 3.5 + - - +
57B SER* 2.9 34.9 + - - +
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Residues in contact with SER 54 (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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30A ARG* 5.9 0.9 + - - -
50A ASN* 3.7 27.9 + - - +
52B SER* 3.1 4.4 - - - -
53B GLN* 1.3 76.3 - - - +
55B ASN* 1.3 65.6 + - - +
57B SER* 3.3 7.2 + - - -
58B HIS* 3.1 23.7 + - - +
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Residues in contact with ASN 55 (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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27A ASN* 2.9 29.9 + - - +
30A ARG* 6.1 0.9 - - - +
50A ASN 4.8 0.2 + - - -
51A LEU* 4.0 7.6 - - + -
55A ASN* 3.3 12.8 - - - +
504A ZN 3.3 21.4 - - - -
27B ASN* 4.6 5.4 + - - +
51B LEU* 4.6 10.3 - - + +
52B SER* 3.1 23.9 + - - +
54B SER* 1.3 74.9 - - - +
56B VAL* 1.3 65.0 + - - +
58B HIS* 3.1 7.6 + - - +
59B GLN* 2.9 48.5 + - - +
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Residues in contact with VAL 56 (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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31B ILE* 4.6 6.7 - - + -
42B VAL* 3.9 16.2 - - + +
45B ILE* 4.0 23.3 - - + -
46B SER* 3.9 25.1 - - - +
51B LEU* 3.9 19.1 - - + -
52B SER 3.0 15.1 + - - +
53B GLN 3.4 7.9 - - - +
55B ASN* 1.3 77.2 - - - +
57B SER* 1.3 58.4 + - - +
59B GLN* 3.3 6.7 + - - +
60B LEU* 2.9 48.4 + - + +
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Residues in contact with SER 57 (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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42B VAL* 3.6 17.9 - - - +
53B GLN* 2.9 20.7 + - - +
54B SER* 3.3 7.6 + - - -
56B VAL* 1.3 73.7 - - - +
58B HIS* 1.3 58.1 + - - +
60B LEU* 3.2 11.2 + - - +
61B LYS* 2.9 30.0 + - - +
80B TYR* 6.2 0.2 - - - -
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Residues in contact with HIS 58 (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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26A TYR* 3.3 49.0 - + + +
27A ASN* 5.1 1.6 - - - -
54B SER 3.1 10.3 + - - +
55B ASN* 3.1 13.2 + - - +
57B SER* 1.3 79.9 - - - +
59B GLN* 1.3 87.0 + - - +
61B LYS* 3.4 20.7 + - + +
62B LEU* 3.4 12.1 + - + +
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Residues in contact with GLN 59 (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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26A TYR* 6.2 0.4 - - - +
27A ASN* 3.9 7.1 - - - +
25B ASP* 5.1 2.2 - - - +
27B ASN* 5.7 4.7 - - + -
28B ARG* 3.1 46.2 + - + +
31B ILE* 4.2 21.1 - - + -
51B LEU* 6.4 0.2 - - + -
55B ASN* 2.9 45.9 + - - +
56B VAL 3.7 3.8 - - - +
58B HIS* 1.3 95.5 - - - +
60B LEU* 1.3 61.4 + - - +
62B LEU* 3.2 7.4 + - - +
63B LEU* 2.9 33.7 + - + +
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Residues in contact with LEU 60 (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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31B ILE* 4.1 24.5 - - + -
35B LEU* 4.5 8.5 - - + -
42B VAL* 3.8 14.1 - - + -
45B ILE* 4.1 7.0 - - + -
56B VAL* 2.9 37.9 + - + +
57B SER* 3.2 6.0 + - - +
59B GLN* 1.3 74.2 - - + +
61B LYS* 1.3 61.3 + - - +
63B LEU* 3.9 6.6 - - + +
64B LYS* 2.8 33.1 + - - +
69B VAL* 3.9 11.5 - - + +
80B TYR* 3.8 52.0 - - + +
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Residues in contact with LYS 61 (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 SER 2.9 13.4 + - - +
58B HIS* 3.5 18.8 - - + +
60B LEU* 1.3 78.2 - - - +
62B LEU* 1.3 57.6 + - - +
64B LYS* 3.8 6.8 - - - +
65B SER* 3.0 28.6 + - - -
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Residues in contact with LEU 62 (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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22B ALA* 4.6 15.7 - - + -
28B ARG* 3.6 42.6 - - - +
58B HIS* 3.4 8.7 + - + +
59B GLN* 3.2 10.2 + - - +
60B LEU 3.2 0.2 - - - -
61B LYS* 1.3 76.5 - - - +
63B LEU* 1.3 66.9 + - - +
64B LYS 3.0 1.3 - - - -
65B SER* 2.8 30.9 + - - +
66B VAL* 3.3 13.4 - - + +
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Residues in contact with LEU 63 (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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22B ALA* 4.1 18.8 - - + +
23B LEU* 4.6 1.8 - - + -
28B ARG* 4.2 21.3 - - + +
31B ILE* 4.4 15.7 - - + -
32B MET* 3.8 32.5 - - + -
59B GLN* 2.9 22.8 + - + +
60B LEU* 3.9 6.3 - - + +
62B LEU* 1.3 76.5 - - - +
64B LYS* 1.3 52.4 + - - +
66B VAL* 3.2 8.8 - - - +
68B LEU* 2.7 64.5 + - + +
69B VAL* 3.9 20.4 - - + -
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Residues in contact with LYS 64 (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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60B LEU 2.8 18.3 + - - +
61B LYS* 3.8 7.4 - - - +
63B LEU* 1.3 74.5 - - - +
65B SER* 1.3 59.4 + - - +
66B VAL 3.1 2.5 - - - -
67B HIS* 2.8 25.5 + - - -
69B VAL* 3.6 24.4 - - + +
70B LYS* 4.7 2.9 - - - +
71B ALA* 4.0 32.9 + - - +
78B MET* 5.9 0.8 - - - +
80B TYR* 4.4 18.9 + - + +
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Residues in contact with SER 65 (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 LYS* 3.0 14.4 + - - -
62B LEU* 2.8 30.6 + - - +
64B LYS* 1.3 76.2 - - - +
66B VAL* 1.3 62.6 + - - +
67B HIS* 3.2 16.1 + - - -
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Residues in contact with VAL 66 (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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18B GLU* 4.1 32.8 - - + +
19B ILE* 4.2 23.6 - - + +
22B ALA* 3.9 10.3 - - + -
62B LEU* 3.3 14.1 - - + +
63B LEU 3.2 16.8 - - - +
65B SER* 1.3 84.7 - - - +
67B HIS* 1.3 75.8 + - - +
68B LEU* 3.3 25.3 + - + +
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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