Contacts of the helix formed by residues 26 - 37 (chain M) in PDB entry 5OXV
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 PRO 26 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-187J G 4.1 6.3 - - - +
18M SER* 3.6 7.0 - - - +
24M GLN 3.9 0.2 - - - -
25M PHE* 1.4 83.9 - - + -
27M VAL* 1.3 64.8 + - - +
28M GLY 3.1 2.7 - - - +
29M ARG* 3.6 26.5 - - + +
30M VAL* 3.3 24.2 + - + +
34N TYR* 4.5 13.0 - - + -
37N TYR* 3.4 55.9 - - + +
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Residues in contact with VAL 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ARG* 3.8 31.9 + - + +
18M SER* 3.3 28.3 + - - +
23M LEU* 4.0 18.6 - - + -
25M PHE 2.8 17.9 + - - +
26M PRO* 1.3 71.8 - - - +
28M GLY* 1.3 63.1 + - - +
30M VAL* 3.9 1.0 + - - +
31M HIS* 3.5 14.0 + - - +
48M PRO* 3.7 18.7 - - + +
49M VAL* 3.2 30.5 - - + -
52M ALA* 4.5 8.7 - - + -
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Residues in contact with GLY 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I A 4.2 15.7 - - - -
192I T 3.9 12.1 + - - -
17M ARG* 3.6 20.4 - - - -
26M PRO* 3.1 1.4 - - - +
27M VAL* 1.3 74.3 - - - +
29M ARG* 1.3 66.2 + - - +
30M VAL 3.0 1.1 - - - -
31M HIS* 2.7 18.4 + - - +
32M ARG* 3.1 9.8 + - - +
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Residues in contact with ARG 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I A 5.6 1.2 + - - -
191I A 3.5 19.8 + - - -
-187J G 3.0 32.7 + - - -
-186J C 2.8 17.5 + - - -
26M PRO* 3.6 26.6 - - + +
28M GLY* 1.3 71.8 - - - +
30M VAL* 1.3 62.8 + - + +
32M ARG* 3.3 20.8 + - - +
33M LEU* 3.1 32.8 + - + +
30N ARG* 5.5 0.4 - - - +
32N GLU* 3.6 34.7 + - - +
33N SER 2.2 35.8 + - - +
34N TYR* 5.2 9.9 - - + -
37N TYR* 3.7 21.2 + - - -
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Residues in contact with VAL 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M PHE* 6.0 1.1 - - + -
26M PRO* 3.3 18.5 + - + +
27M VAL 4.0 1.8 - - - +
28M GLY 2.9 3.0 + - - -
29M ARG* 1.3 78.8 - - + +
31M HIS* 1.3 63.1 + - - +
33M LEU* 3.2 2.9 + - - +
34M LEU* 3.1 32.4 + - + +
48M PRO* 3.7 31.2 - - + +
51M LEU* 4.2 11.2 - - + -
52M ALA* 4.0 18.8 - - + +
55M LEU* 4.8 5.4 - - + -
34N TYR* 4.7 13.7 - - + +
67N PHE* 4.0 24.5 - - + -
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Residues in contact with HIS 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-196J A 4.4 0.8 + - - -
17M ARG* 4.1 20.9 - - - +
27M VAL 3.5 6.7 + - - +
28M GLY* 2.7 13.4 + - - +
30M VAL* 1.3 72.1 - - - +
32M ARG* 1.3 66.8 + - - +
34M LEU* 4.1 2.8 - - - +
35M ARG* 3.1 60.6 + - - +
43M VAL* 3.4 40.2 + - + +
44M GLY 3.4 12.6 - - - -
45M ALA* 5.0 2.7 - - - -
48M PRO* 3.4 28.4 - - + +
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Residues in contact with ARG 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I A 3.3 16.0 + - - -
191I A 2.7 47.3 + - - +
28M GLY 3.1 5.8 + - - +
29M ARG* 3.3 24.5 + - - +
31M HIS* 1.3 77.9 - - - +
33M LEU* 1.3 75.8 - - + +
35M ARG* 3.1 9.9 + - - +
36M LYS* 3.0 56.6 + - + +
32N GLU* 2.3 47.0 + - - -
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Residues in contact with LEU 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M ARG* 3.1 23.8 + - + +
30M VAL 3.2 2.0 + - - +
32M ARG* 1.3 103.7 - - + +
34M LEU* 1.3 55.6 + - - +
36M LYS* 4.8 7.2 - - + -
37M GLY* 2.9 28.7 + - - +
39M TYR* 3.6 4.3 - - - -
32N GLU* 5.3 0.7 - - - +
34N TYR* 4.2 20.2 - - + +
64N ASN* 5.9 2.7 - - - +
67N PHE* 3.6 25.7 - - + -
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Residues in contact with LEU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M VAL* 3.1 33.4 + - + +
31M HIS* 4.1 3.6 - - - +
32M ARG 3.3 0.2 - - - -
33M LEU* 1.3 76.7 - - - +
35M ARG* 1.3 63.8 + - - +
37M GLY 3.7 1.0 + - - -
38M ASN 4.0 1.9 + - - -
39M TYR* 3.1 34.2 + - + +
40M ALA 5.0 1.0 + - - +
43M VAL* 4.1 28.6 - - + +
47M ALA* 4.5 6.7 - - + -
48M PRO* 4.0 20.6 - - + -
51M LEU* 4.1 14.8 - - + -
67N PHE* 4.0 17.3 - - + -
71N ALA* 4.2 18.6 - - + -
86N ILE* 5.3 7.9 - - + -
91N ILE* 4.9 7.6 - - + -
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Residues in contact with ARG 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-196J A 2.2 62.6 + - - +
-195J C 4.9 5.5 - - - +
31M HIS* 3.1 47.8 + - - +
32M ARG* 3.1 9.0 + - - +
34M LEU* 1.3 79.4 - - - +
36M LYS* 1.3 63.7 + - + +
38M ASN* 3.9 8.8 + - - +
40M ALA 4.8 6.5 - - - +
41M GLU 5.9 1.3 - - - +
43M VAL* 3.8 21.5 - - + -
41Q GLU* 5.5 2.4 - - - +
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Residues in contact with LYS 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M ARG* 3.0 42.7 + - + +
33M LEU* 4.5 7.0 - - + +
35M ARG* 1.3 78.0 - - + +
37M GLY* 1.3 55.9 + - - +
38M ASN* 3.2 24.9 + - - -
41Q GLU* 5.8 2.1 - - - +
79R HIS* 3.6 5.3 + - - -
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Residues in contact with GLY 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M LEU* 2.9 20.9 + - - +
34M LEU 3.7 0.2 + - - -
35M ARG 3.5 0.6 - - - -
36M LYS* 1.3 74.1 - - - +
38M ASN* 1.3 70.8 + - - +
39M TYR* 3.4 27.8 + - - -
79R HIS* 3.5 19.1 + - - -
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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