Contacts of the helix formed by residues 26 - 36 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283I G 3.7 10.3 - - - +
-279J G 6.5 0.2 - - - -
18Q SER* 3.6 7.0 - - - +
24Q GLN 3.9 0.4 - - - -
25Q PHE* 1.4 87.2 - - + +
27Q VAL* 1.3 59.6 + - - +
28Q GLY 3.1 2.2 - - - +
29Q ARG* 3.1 25.1 + - + +
30Q VAL* 3.1 28.4 + - + +
34R TYR* 4.7 5.6 - - + -
37R TYR* 3.1 55.9 - - + +
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Residues in contact with VAL 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q ARG* 3.9 27.5 + - + +
18Q SER* 3.4 32.8 + - - +
21Q ALA* 5.0 1.3 - - + -
23Q LEU* 4.5 11.2 - - + -
25Q PHE 3.6 6.7 - - - +
26Q PRO* 1.3 68.5 - - - +
28Q GLY* 1.3 63.3 + - - +
29Q ARG 3.4 0.2 - - - -
30Q VAL* 4.0 1.8 - - - -
31Q HIS* 3.2 22.5 + - - +
48Q PRO* 3.9 8.3 - - + +
49Q VAL* 3.7 42.4 - - + +
52Q ALA* 4.3 14.4 - - + -
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Residues in contact with GLY 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-279J G 4.1 30.1 + - - +
-278J A 4.1 6.3 + - - -
17Q ARG* 3.8 17.9 + - - +
18Q SER* 5.1 0.2 + - - -
26Q PRO* 3.1 1.6 - - - +
27Q VAL* 1.3 77.4 - - - +
29Q ARG* 1.3 63.9 + - - +
31Q HIS* 3.1 3.6 + - - +
32Q ARG* 3.0 23.0 + - - +
35Q ARG* 5.4 0.2 + - - -
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Residues in contact with ARG 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I G 3.5 26.5 + - - -
284I C 2.5 22.4 + - - -
-279J G 3.6 16.8 + - - +
26Q PRO* 3.1 26.7 + - + +
28Q GLY* 1.3 71.4 - - - +
30Q VAL* 1.3 56.0 + - + +
31Q HIS 2.7 14.6 + - - -
32Q ARG* 2.9 32.8 + - - +
33Q LEU* 3.0 24.4 + - + +
32R GLU* 3.6 26.8 + - - +
33R SER 2.7 39.2 + - - +
34R TYR* 4.7 14.1 - - + -
37R TYR* 3.8 13.8 + - - -
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Residues in contact with VAL 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q PHE* 5.5 1.3 - - + -
26Q PRO* 3.1 17.0 + - + +
27Q VAL 4.2 4.5 - - - +
29Q ARG* 1.3 76.2 - - + +
31Q HIS* 1.3 59.7 + - - +
33Q LEU* 4.1 8.8 - - - +
34Q LEU* 3.0 27.0 + - + +
48Q PRO* 3.7 15.5 - - + +
51Q LEU* 3.6 34.5 - - + -
52Q ALA* 3.8 22.9 - - + -
55Q LEU* 4.5 13.7 - - + -
34R TYR* 4.8 11.7 - - + +
67R PHE* 3.8 7.0 - - + -
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Residues in contact with HIS 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I A 4.7 5.9 + - - -
17Q ARG* 3.3 34.1 + - - +
27Q VAL 3.2 18.5 + - - +
28Q GLY 3.1 6.2 + - - +
29Q ARG 2.7 2.2 + - - -
30Q VAL* 1.3 76.7 - - - +
32Q ARG* 1.3 66.4 + - - +
34Q LEU* 3.4 10.1 + - - +
35Q ARG* 2.8 48.2 + - - +
43Q VAL* 4.1 16.2 - - + +
44Q GLY 3.7 21.1 - - - -
45Q ALA* 5.0 3.6 - - + +
48Q PRO* 3.2 19.2 - - + +
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Residues in contact with ARG 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-280J G 3.7 12.5 + - - -
-279J G 3.2 37.2 + - - +
28Q GLY 3.0 11.1 + - - +
29Q ARG* 2.9 16.6 + - - +
31Q HIS* 1.3 76.3 - - - +
33Q LEU* 1.3 90.6 + - - +
35Q ARG* 2.9 19.3 + - - +
36Q LYS* 2.9 49.9 + - + +
32R GLU* 2.3 46.2 + - - -
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Residues in contact with LEU 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q ARG* 3.0 27.4 + - + +
30Q VAL* 4.2 4.7 - - - +
32Q ARG* 1.3 104.7 - - - +
34Q LEU* 1.3 63.3 + - - +
35Q ARG 3.0 1.6 + - - -
36Q LYS* 3.3 22.9 + - - +
37Q GLY* 3.4 4.7 + - - -
39Q TYR* 3.9 2.1 + - - -
34R TYR* 3.4 26.2 - - + +
64R ASN* 5.7 2.7 - - - +
67R PHE* 3.6 30.5 - - + -
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Residues in contact with LEU 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q VAL* 3.0 28.3 + - + +
31Q HIS 3.9 5.2 - - - +
32Q ARG 3.3 0.6 - - - -
33Q LEU* 1.3 77.9 - - - +
35Q ARG* 1.3 60.9 + - - +
38Q ASN 4.3 1.4 + - - -
39Q TYR* 3.1 35.5 + - + +
40Q ALA 5.2 2.1 + - - +
43Q VAL* 4.1 27.3 - - + +
47Q ALA* 4.8 2.2 - - + -
48Q PRO* 4.1 17.5 - - + -
51Q LEU* 3.8 22.0 - - + -
67R PHE* 4.0 9.2 - - + -
71R ALA* 4.3 22.0 - - + -
86R ILE* 4.6 19.1 - - + -
91R ILE* 4.5 9.0 - - + -
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Residues in contact with ARG 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I A 3.5 31.9 + - - +
275I G 5.7 2.0 - - - -
28Q GLY 5.4 0.2 + - - -
31Q HIS* 2.8 54.9 + - - +
32Q ARG* 2.9 22.0 + - - +
34Q LEU* 1.3 75.8 - - - +
36Q LYS* 1.3 66.1 + - + +
37Q GLY 2.6 17.0 + - - -
38Q ASN* 3.4 12.1 + - - +
40Q ALA 5.5 3.8 - - - +
41Q GLU 5.3 5.2 - - - +
43Q VAL* 3.7 20.2 - - + -
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Residues in contact with LYS 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N HIS* 4.3 9.8 + - - -
32Q ARG* 2.9 40.0 + - + +
33Q LEU* 3.4 9.7 - - - +
35Q ARG* 1.3 84.4 - - - +
37Q GLY* 1.3 54.9 + - - -
38Q ASN* 4.7 5.2 - - - +
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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