Contacts of the helix formed by residues 25 - 38 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU 2.7 9.1 + - - +
24A GLY* 1.3 75.6 - - - +
26A TYR* 1.3 68.5 + - - +
27A ASN* 3.0 15.6 + - - +
28A ARG* 2.9 67.2 + - + +
29A ILE* 2.9 26.6 + - - +
59A GLN* 4.8 2.4 - - - +
25B ASP* 4.1 13.2 - - - +
28B ARG* 4.9 8.3 + - - -
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Residues in contact with TYR 26 (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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25A ASP* 1.3 73.8 - - - +
27A ASN* 1.3 69.7 + - - +
29A ILE* 3.3 10.1 + - + +
30A ARG* 3.0 62.6 + - + +
58B HIS* 3.3 40.8 - + + +
59B GLN* 6.2 0.4 - - - +
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Residues in contact with ASN 27 (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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25A ASP* 3.0 9.4 + - - +
26A TYR* 1.3 87.6 - - - +
28A ARG* 1.3 61.0 + - + +
30A ARG* 3.1 31.6 + - - +
31A ILE* 3.0 33.0 + - + +
51A LEU* 3.7 20.5 - - + +
55A ASN* 4.6 4.6 + - - +
59A GLN* 5.6 6.1 - - + -
55B ASN* 2.9 37.0 + - - +
58B HIS* 5.1 1.1 - - - -
59B GLN* 3.9 9.1 - - - +
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Residues in contact with ARG 28 (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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21A LYS 3.5 22.6 + - - -
22A ALA* 2.5 30.8 + - - +
23A LEU* 5.1 1.6 - - - -
24A GLY 4.5 1.8 + - - -
25A ASP* 2.9 43.8 + - - +
27A ASN* 1.3 76.6 - - - +
29A ILE* 1.3 59.1 + - - +
31A ILE* 3.3 9.2 + - - +
32A MET* 2.9 34.7 + - - +
59A GLN* 3.0 40.6 + - + +
62A LEU* 3.6 25.0 - - - +
63A LEU* 4.0 24.6 - - + +
25B ASP* 4.8 7.3 + - - -
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Residues in contact with ILE 29 (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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23A LEU* 2.9 50.5 - - + +
25A ASP 2.9 14.0 + - - +
26A TYR* 3.4 13.5 - - + +
28A ARG* 1.3 75.1 - - - +
30A ARG* 1.3 60.7 + - + +
32A MET* 3.7 2.9 - - - +
33A GLU* 2.8 32.1 + - + +
91A LEU* 4.8 12.5 - - + +
95A ILE* 4.9 17.0 - - + -
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Residues in contact with ARG 30 (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 TYR* 3.0 51.0 + - + +
27A ASN* 3.1 32.3 + - - +
29A ILE* 1.3 79.0 - - + +
31A ILE* 1.3 60.9 + - - +
33A GLU* 3.9 6.8 - - - +
34A LEU* 3.1 24.4 + - - +
49A LEU* 3.2 59.8 + - + +
50A ASN 4.9 0.6 + - - -
51A LEU* 3.7 14.9 - - - +
54B SER* 5.9 0.6 + - - -
55B ASN* 6.1 1.2 - - - +
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Residues in contact with ILE 31 (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 ASN 3.0 19.9 + - - +
28A ARG* 3.6 9.2 - - - +
30A ARG* 1.3 75.2 - - - +
32A MET* 1.3 65.0 + - - +
34A LEU* 3.4 3.0 + - - +
35A LEU* 3.0 32.6 + - + +
45A ILE* 4.1 14.8 - - + -
49A LEU* 3.7 19.5 - - + -
51A LEU* 4.5 8.3 - - + -
56A VAL* 4.5 20.4 - - + +
59A GLN* 3.9 31.9 - - + -
60A LEU* 3.9 24.2 - - + -
63A LEU* 4.4 8.1 - - + -
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Residues in contact with MET 32 (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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23A LEU* 3.8 29.6 - - + -
28A ARG 2.9 24.3 + - - +
29A ILE* 3.3 5.6 + - - +
31A ILE* 1.3 76.6 - - - +
33A GLU* 1.3 50.7 + - - +
35A LEU* 3.1 6.7 + - - +
36A SER* 2.8 35.2 + - - -
63A LEU* 3.9 16.6 - - + -
68A LEU* 3.9 13.2 - - + +
69A VAL* 3.7 27.8 - - - -
82A LEU* 3.8 8.5 - - + +
87A VAL* 3.7 30.3 - - + -
90A MET* 5.3 1.3 - - + -
91A LEU* 3.6 22.5 - - + +
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Residues in contact with GLU 33 (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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29A ILE* 2.8 22.4 + - + +
30A ARG* 3.9 7.0 - - - +
32A MET* 1.3 75.9 - - - +
34A LEU* 1.3 69.0 + - - +
36A SER* 2.7 28.4 + - - +
37A VAL* 3.4 19.7 + - - +
91A LEU* 3.9 7.5 - - + +
95A ILE* 4.9 20.6 - - + -
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Residues in contact with LEU 34 (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 ARG 3.1 15.5 + - - +
31A ILE 3.7 3.6 - - - +
33A GLU* 1.3 85.7 + - - +
35A LEU* 1.3 68.9 + - + +
37A VAL* 3.0 20.6 + - + +
38A SER* 3.1 20.0 + - - +
40A ALA* 5.5 0.4 - - + -
44A HIS* 4.7 9.2 - - + +
45A ILE* 4.0 25.6 - - + +
48A GLN* 3.4 45.3 - - + +
49A LEU* 3.9 26.7 - - + -
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Residues in contact with LEU 35 (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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31A ILE* 3.0 25.3 + - + +
32A MET* 3.4 8.1 - - - +
34A LEU* 1.3 80.6 - - + +
36A SER* 1.3 60.9 + - - +
37A VAL 3.0 1.0 + - - -
38A SER 3.4 22.9 + - - +
39A GLU* 4.1 1.7 + - - -
40A ALA* 4.7 3.6 - - + +
45A ILE* 3.7 31.4 - - + -
60A LEU* 4.6 1.8 - - + -
69A VAL* 3.7 31.2 - - + -
80A TYR* 4.1 14.8 - - + +
81A SER* 3.9 28.5 - - - +
82A LEU* 3.6 18.3 + - + +
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Residues in contact with SER 36 (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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32A MET 2.8 12.7 + - - -
33A GLU* 2.7 26.3 + - - +
35A LEU* 1.3 75.8 - - - +
37A VAL* 1.3 64.0 + - - +
82A LEU* 3.6 22.4 - - - +
91A LEU* 3.9 12.2 - - - +
92A LYS* 4.1 33.7 + - - +
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Residues in contact with VAL 37 (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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33A GLU* 3.7 27.6 - - - +
34A LEU* 3.0 14.2 + - + +
35A LEU 4.0 0.2 - - - -
36A SER* 1.3 84.2 + - - +
38A SER* 1.3 66.6 + - - +
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Residues in contact with SER 38 (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 LEU* 3.1 21.8 + - - +
35A LEU* 3.4 14.6 + - - +
37A VAL* 1.3 89.8 - - - +
39A GLU* 1.3 75.2 + - - +
40A ALA* 3.7 5.8 + - - +
44A HIS* 5.7 4.6 + - - -
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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