Contacts of the helix formed by residues 25 - 38 (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 ASP 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASP* 4.1 14.3 - - - +
28A ARG* 4.8 6.6 + - - -
59A GLN* 5.7 2.9 + - - -
23B LEU 2.8 8.5 + - - +
24B GLY* 1.3 75.8 - - - +
26B TYR* 1.3 67.5 + - - +
27B ASN* 3.5 12.1 + - - +
28B ARG* 3.0 63.0 + - + +
29B ILE* 3.0 29.8 + - - +
59B GLN* 4.7 2.6 - - - +
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Residues in contact with TYR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 3.5 43.7 - + + +
59A GLN* 6.1 0.4 - - - +
25B ASP* 1.3 76.3 + - - +
27B ASN* 1.3 69.9 + - - +
29B ILE* 3.3 7.8 + - + +
30B ARG* 3.0 64.7 + - + +
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 3.0 37.5 + - - +
58A HIS* 5.5 1.3 - - - -
59A GLN* 3.9 9.7 - - - +
25B ASP* 3.4 10.5 + - - +
26B TYR* 1.3 83.6 - - - +
28B ARG* 1.3 66.1 + - + +
30B ARG* 2.9 34.9 + - - +
31B ILE* 3.0 31.7 + - + +
49B LEU* 4.8 0.3 - - - +
51B LEU* 4.1 16.5 - - + +
55B ASN* 4.6 5.0 + - - +
59B GLN* 5.7 4.9 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP* 4.9 7.9 + - - -
21B LYS 3.6 15.2 + - - -
22B ALA 2.5 31.0 + - - +
23B LEU* 5.3 2.0 - - - -
24B GLY 4.3 3.6 + - - -
25B ASP* 3.0 47.3 + - + +
26B TYR 3.4 0.4 - - - -
27B ASN* 1.3 76.9 - - - +
29B ILE* 1.3 58.7 + - - +
31B ILE* 3.3 9.7 + - - +
32B MET* 2.9 33.8 + - - +
59B GLN* 3.1 41.0 + - + +
62B LEU* 3.6 28.2 - - - +
63B LEU* 4.2 21.6 - - + +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.1 37.9 - - + +
24B GLY* 5.2 0.4 - - - -
25B ASP 3.0 18.9 + - - +
26B TYR* 3.6 8.3 - - + +
28B ARG* 1.3 76.6 - - - +
30B ARG* 1.3 62.3 + - + +
32B MET* 3.6 6.4 - - - +
33B GLU* 2.7 32.3 + - + +
91B LEU* 5.1 12.5 - - + +
95B ILE* 6.0 5.2 - - + -
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 5.7 1.4 + - - -
55A ASN* 6.2 0.4 - - - +
26B TYR* 3.0 48.8 + - + +
27B ASN* 2.9 34.0 + - - +
29B ILE* 1.3 77.9 - - + +
31B ILE* 1.3 57.2 - - - +
33B GLU* 3.3 11.5 + - + +
34B LEU* 2.9 28.6 + - - +
49B LEU* 3.2 59.1 + - + +
50B ASN* 5.0 1.2 + - - -
51B LEU* 3.5 17.9 - - - +
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Residues in contact with ILE 31 (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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27B ASN* 3.0 20.5 + - + +
28B ARG* 3.5 9.2 - - - +
30B ARG* 1.3 73.5 - - - +
32B MET* 1.3 65.0 + - - +
34B LEU* 3.2 4.7 + - - +
35B LEU* 2.9 31.7 + - + +
45B ILE* 4.1 20.6 - - + -
49B LEU* 3.4 22.7 - - + -
51B LEU* 4.4 13.5 - - + -
56B VAL* 4.6 13.2 - - + +
59B GLN* 4.2 28.3 - - + -
60B LEU* 4.1 23.1 - - + -
63B LEU* 4.4 7.0 - - + -
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Residues in contact with MET 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.0 29.4 - - + -
28B ARG 2.9 22.5 + - - +
29B ILE* 3.6 5.6 - - - +
31B ILE* 1.3 76.2 - - - +
33B GLU* 1.3 59.2 + - - +
35B LEU* 3.2 4.6 + - - +
36B SER* 2.9 24.4 + - - -
63B LEU* 3.8 18.8 - - + -
68B LEU* 3.9 10.3 - - + +
69B VAL* 3.7 26.0 - - - -
82B LEU* 3.6 14.9 - - + +
87B VAL* 3.5 31.6 - - + -
90B MET* 5.5 0.7 - - + -
91B LEU* 3.5 26.9 - - + +
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Residues in contact with GLU 33 (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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29B ILE* 2.7 21.6 + - + +
30B ARG* 3.3 11.9 - - + +
32B MET* 1.3 76.3 - - - +
34B LEU* 1.3 65.6 + - - +
36B SER* 2.4 28.4 + - - -
37B VAL* 3.5 16.1 + - - +
49B LEU* 6.3 0.4 - - + -
91B LEU* 4.0 7.6 - - + +
95B ILE* 4.0 25.0 - - + +
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Residues in contact with LEU 34 (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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30B ARG 2.9 13.4 + - - +
31B ILE* 3.2 8.9 + - - +
33B GLU* 1.3 78.1 - - + +
35B LEU* 1.3 75.1 + - + +
37B VAL* 3.0 19.9 + - - +
38B SER* 3.3 20.7 + - - +
40B ALA* 4.2 13.2 - - + -
44B HIS* 4.5 11.2 - - + +
45B ILE* 4.0 17.7 - - + -
48B GLN* 4.0 25.1 - - + -
49B LEU* 3.7 30.3 - - + -
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Residues in contact with LEU 35 (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* 2.9 28.9 + - + +
32B MET* 3.2 8.7 + - - +
34B LEU* 1.3 87.2 - - + +
36B SER* 1.3 61.9 + - - +
37B VAL 3.2 0.7 + - - -
38B SER* 3.3 25.6 + - - +
39B GLU* 4.0 1.4 + - - -
40B ALA 4.2 4.5 - - - +
45B ILE* 4.2 19.1 - - + -
60B LEU* 4.5 9.4 - - + -
69B VAL* 3.8 28.5 - - + -
80B TYR* 4.0 26.5 - - + +
81B SER* 4.1 9.9 - - - -
82B LEU* 3.7 21.0 + - + +
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Residues in contact with SER 36 (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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32B MET 2.9 13.5 + - - -
33B GLU* 2.4 32.3 + - - -
35B LEU* 1.3 77.1 - - - +
37B VAL* 1.3 62.4 + - - +
82B LEU* 3.7 21.7 - - - +
91B LEU* 4.0 10.1 - - - +
92B LYS* 4.1 31.6 + - - +
95B ILE* 5.4 2.6 - - - +
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 3.8 25.1 - - - +
34B LEU* 3.0 11.3 + - + +
36B SER* 1.3 82.7 - - - +
38B SER* 1.3 69.6 + - - +
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Residues in contact with SER 38 (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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34B LEU* 3.3 15.3 + - - +
35B LEU* 3.3 15.7 + - - +
37B VAL* 1.3 92.4 - - - +
39B GLU* 1.3 75.1 + - - +
40B ALA* 4.1 3.6 - - - +
44B HIS* 5.7 4.5 - - - -
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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