Contacts of the helix formed by residues 26 - 39 (chain A) in PDB entry 1RQG
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 TYR 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 3.4 27.1 - - - -
9A ALA* 2.4 30.2 + - - +
11A PRO* 3.0 22.5 - - + +
17A ILE* 4.6 2.7 - - + -
21A HIS* 3.3 42.0 - - + -
22A LEU* 3.1 19.1 + - + -
25A ALA* 1.3 82.2 - - + +
27A LEU* 1.3 63.7 + - - +
28A PRO* 3.2 1.3 - - - -
29A ALA* 3.1 4.0 + - - +
30A ASP* 2.8 29.8 + - - +
47A CYS* 3.9 6.3 - - - -
82A PHE* 3.6 31.4 - + + -
87A ILE* 4.2 11.8 - - + +
89A PHE* 3.8 11.9 - + - -
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Residues in contact with LEU 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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22A LEU* 2.9 21.9 + - + +
23A ALA* 4.5 4.0 - - - -
26A TYR* 1.3 76.0 - - - +
28A PRO* 1.3 72.6 - - + +
30A ASP* 3.2 1.4 + - + +
31A ILE* 3.0 32.8 + - + +
87A ILE* 4.2 7.7 - - + +
368A ARG* 3.8 59.9 - - + +
371A LEU* 3.7 36.6 - - + -
372A THR* 3.8 11.2 - - - +
375A MET* 4.8 3.8 - - + -
507A PHE 5.2 0.4 - - - +
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Residues in contact with PRO 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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22A LEU 3.3 10.3 - - - +
23A ALA 3.2 18.2 - - - +
24A GLY 4.3 6.7 - - - +
25A ALA 3.8 0.2 - - - -
26A TYR 3.4 9.0 - - - +
27A LEU* 1.3 95.9 - - + +
29A ALA* 1.3 62.9 + - - +
31A ILE* 3.1 3.9 + - + +
32A PHE* 3.0 22.7 + - - +
294A PHE* 3.5 23.6 - - + -
335A ASN* 3.5 14.8 - - - +
375A MET* 3.8 17.5 - - + -
452A PHE* 3.7 17.9 - - + -
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Residues in contact with ALA 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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6A VAL* 4.6 0.7 - - + -
7A THR 4.5 0.4 - - - +
8A SER* 3.3 26.7 - - - +
25A ALA 3.5 6.1 - - - +
26A TYR 3.1 6.0 + - - +
28A PRO* 1.3 80.9 - - - +
30A ASP* 1.3 56.8 + - - +
32A PHE* 3.6 0.7 - - - +
33A VAL* 2.9 36.4 + - - +
45A PHE* 3.6 13.9 - - + -
294A PHE* 3.3 29.7 - - + -
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Residues in contact with ASP 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 2.8 18.8 + - - +
27A LEU 3.6 5.4 - - - +
29A ALA* 1.3 69.8 - - - +
31A ILE* 1.3 60.8 + - - +
33A VAL* 3.3 0.9 + - - +
34A ARG* 2.7 48.0 + - - +
45A PHE* 4.1 8.6 - - - -
86A LYS 2.9 6.6 - - - +
87A ILE* 3.3 17.0 - - + +
88A SER* 2.7 37.4 + - - -
368A ARG* 2.5 36.3 + - - +
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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 LEU* 3.0 29.8 + - + +
28A PRO 3.5 6.1 - - - +
30A ASP* 1.3 75.7 - - - +
32A PHE* 1.3 62.2 + - - +
35A TYR* 3.3 21.8 + - - +
372A THR* 3.5 31.9 - - + +
375A MET* 4.0 19.1 - - + -
447A ILE* 4.2 6.7 - - + +
452A PHE* 3.5 21.5 - - + -
506A PRO* 3.5 31.3 - - + +
507A PHE* 4.1 30.1 - - + -
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Residues in contact with PHE 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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4A TYR* 4.6 6.5 - + - -
6A VAL* 4.4 15.5 - - + -
28A PRO 3.0 15.8 + - - +
29A ALA 3.6 3.8 - - - +
31A ILE* 1.3 75.7 - - - +
33A VAL* 1.3 67.0 + - + +
35A TYR* 3.3 5.9 - - - +
36A LEU* 3.0 49.0 + - + +
292A ILE* 4.5 11.9 - - + -
294A PHE* 3.6 24.9 - + + -
447A ILE* 3.7 26.5 - - + -
448A MET* 3.9 36.3 - - + -
450A TYR* 3.7 31.2 - + - -
452A PHE* 4.3 3.6 - + + -
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Residues in contact with VAL 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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6A VAL* 3.7 35.0 - - + -
29A ALA 2.9 19.3 + - - +
30A ASP 4.0 1.8 - - - +
32A PHE* 1.3 74.9 - - + +
34A ARG* 1.3 66.5 + - - +
36A LEU* 3.1 8.8 + - - +
37A ARG* 2.9 48.1 + - - +
43A VAL* 4.0 15.7 - - + +
45A PHE* 3.7 35.4 - - + -
88A SER* 5.6 0.4 - - - +
90A ASP* 5.3 0.2 - - - +
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Residues in contact with ARG 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 ASP* 2.7 37.2 + - - +
31A ILE 4.1 0.2 - - - +
33A VAL* 1.3 71.1 - - - +
35A TYR* 1.3 66.3 + - - +
37A ARG* 2.9 19.3 + - - +
38A LEU* 2.9 26.3 + - - +
86A LYS* 2.7 32.7 + - - +
88A SER* 3.5 28.6 + - - +
368A ARG* 3.5 3.6 - - - +
505A GLU* 3.1 33.2 + - + +
506A PRO* 3.5 37.5 - - + -
509A PRO* 3.3 22.8 - - - +
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Residues in contact with TYR 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 3.3 13.3 + - - +
32A PHE 3.3 8.7 - - - +
33A VAL 3.2 0.2 - - - -
34A ARG* 1.3 77.6 - - - +
36A LEU* 1.3 74.9 + - + +
38A LEU* 2.8 17.7 + - - +
39A LYS* 2.8 49.9 + - + +
444A GLY* 3.5 24.4 + - - -
447A ILE* 3.7 28.9 - - + -
448A MET* 3.6 36.4 - - + +
506A PRO* 4.1 9.1 - - + +
527A TRP* 3.4 48.2 - + - -
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Residues in contact with LEU 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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4A TYR* 3.7 35.4 - - + +
32A PHE* 3.0 44.4 + - + +
33A VAL* 3.4 9.0 - - - +
35A TYR* 1.3 81.9 - - + +
37A ARG* 1.3 59.3 + - - +
39A LYS* 3.2 7.4 + - + +
40A GLY 3.1 3.6 + - - -
41A GLU* 3.0 59.6 + - + +
43A VAL* 3.9 20.0 - - + -
448A MET* 4.1 19.1 - - - -
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Residues in contact with ARG 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 VAL* 2.9 35.5 + - - +
34A ARG* 2.9 25.4 + - - +
36A LEU* 1.3 71.6 - - - +
38A LEU* 1.3 63.1 + - + +
39A LYS 3.0 1.6 - - - -
40A GLY* 2.8 21.0 + - - -
41A GLU 4.8 6.5 - - - +
43A VAL* 4.0 15.4 + - + +
45A PHE* 4.2 0.6 - - - -
88A SER* 2.6 55.8 + - - -
90A ASP* 3.0 22.2 + - - -
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Residues in contact with LEU 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 ARG 2.9 15.3 + - - +
35A TYR 2.8 9.9 + - - +
37A ARG* 1.3 73.2 - - + +
39A LYS* 1.3 60.4 + - - +
40A GLY* 3.1 1.1 + - - -
502A ILE* 4.1 6.3 - - + +
505A GLU* 3.2 36.3 - - + +
506A PRO* 3.5 22.0 - - + -
525A LYS* 3.3 42.8 - - + +
526A ARG* 3.6 7.3 - - - +
527A TRP* 2.9 48.4 + - + +
528A GLU* 3.4 6.9 - - - +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 2.8 46.5 + - + +
36A LEU* 3.2 16.4 - - + +
37A ARG 3.0 0.2 - - - -
38A LEU* 1.3 76.6 - - - +
40A GLY* 1.3 57.9 + - - +
41A GLU* 3.2 25.0 + - - +
527A TRP* 4.2 23.6 - - + +
528A GLU* 4.7 10.7 - - - +
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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