Contacts of the helix formed by residues 24 - 38 (chain C) in PDB entry 1OHV
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 GLY 24 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C THR* 3.6 1.3 - - - -
21C GLU 3.1 16.0 + - - -
22C VAL* 3.7 1.8 - - - +
23C PRO* 1.3 73.8 - - - +
25C PRO* 1.3 73.2 - - - +
27C SER* 3.1 3.7 + - - -
28C ARG* 2.9 32.8 + - - +
59C ASP* 5.0 2.4 + - - -
61C ASP* 3.1 20.0 + - - +
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Residues in contact with PRO 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C THR* 4.2 17.9 - - + +
24C GLY* 1.3 84.0 - - - +
26C ARG* 1.3 56.0 + - - +
28C ARG* 3.3 27.6 + - - +
29C GLU* 3.0 27.9 + - - +
61C ASP* 3.2 13.5 - - - +
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PRO* 1.3 70.1 - - - +
27C SER* 1.3 64.2 + - - +
29C GLU* 3.3 7.7 + - - +
30C LEU* 3.0 28.8 + - + +
60C VAL* 3.8 23.8 - - + +
61C ASP* 2.8 25.0 + - - +
109D GLU* 6.0 0.7 - - - +
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Residues in contact with SER 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO* 3.8 19.5 - - - -
24C GLY 3.1 10.3 + - - -
26C ARG* 1.3 77.8 - - - +
28C ARG* 1.3 55.8 + - - +
30C LEU* 3.1 2.8 + - - +
31C MET* 2.8 36.8 + - - +
45C PHE* 3.5 7.3 - - - +
46C PHE* 3.1 31.9 + - - -
59C ASP* 4.7 2.1 + - - +
60C VAL* 3.2 17.9 + - - +
61C ASP* 3.1 9.4 + - - -
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Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLU* 5.0 5.7 + - - +
23C PRO* 2.9 42.5 + - + +
24C GLY* 2.9 24.9 + - - +
25C PRO* 3.6 31.7 - - - +
27C SER* 1.3 76.0 - - - +
29C GLU* 1.3 57.2 + - - +
31C MET* 3.5 9.6 + - + +
32C LYS* 3.0 27.9 + - - +
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PRO 3.0 14.9 + - - +
26C ARG* 3.5 11.7 - - - +
28C ARG* 1.3 76.4 - - - +
30C LEU* 1.3 63.7 + - + +
32C LYS* 3.3 13.9 + - - +
33C GLN* 2.5 51.9 + - - +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ARG* 3.0 21.2 + - + +
29C GLU* 1.3 73.9 - - + +
31C MET* 1.3 61.2 + - - +
33C GLN* 3.3 27.2 + - - +
34C LEU* 2.9 29.5 + - - +
46C PHE* 3.5 47.4 - - + -
60C VAL* 4.2 8.5 - - + -
109D GLU* 3.9 34.8 - - + +
112D VAL* 4.3 6.6 - - + +
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Residues in contact with MET 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO* 3.9 25.6 - - + -
27C SER* 2.8 30.7 + - - +
28C ARG* 3.7 9.0 - - + +
29C GLU 3.3 0.2 - - - -
30C LEU* 1.3 77.4 - - - +
32C LYS* 1.3 57.3 + - - +
34C LEU* 3.5 3.2 + - - +
35C ASN* 2.9 30.2 + - - +
40C ALA* 4.2 10.7 - - + +
41C GLU 5.9 0.2 - - - +
43C VAL* 3.3 40.6 - - + +
44C HIS 4.0 8.1 - - - +
45C PHE* 4.4 0.9 - - - -
46C PHE* 3.6 18.4 - - + -
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Residues in contact with LYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG 3.0 15.3 + - - +
29C GLU* 3.5 17.9 - - - +
30C LEU 3.2 0.2 - - - -
31C MET* 1.3 77.0 - - - +
33C GLN* 1.3 64.6 + - + +
35C ASN* 3.2 19.2 + - - +
36C ILE* 3.5 16.1 + - + +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU* 2.5 40.7 + - - +
30C LEU* 3.3 27.0 + - - +
32C LYS* 1.3 80.0 - - + +
34C LEU* 1.3 63.6 + - - +
36C ILE* 3.1 27.0 + - - +
37C ILE* 4.2 8.0 + - - +
112D VAL* 4.1 9.4 - - + +
116D ARG* 3.3 37.5 + - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU 2.9 16.5 + - - +
31C MET* 3.8 4.3 - - - +
33C GLN* 1.3 75.3 - - - +
35C ASN* 1.3 57.6 + - - +
36C ILE 3.1 0.2 - - - -
37C ILE* 3.0 25.2 + - + +
38C GLN* 3.3 44.8 + - + +
40C ALA* 4.1 5.2 - - + -
43C VAL* 4.0 23.3 - - + -
46C PHE* 3.7 20.9 - - + -
103D LEU 5.6 1.3 - - - +
107D PRO* 4.4 3.8 - - + -
111D PHE* 4.0 25.8 - - + -
112D VAL* 3.9 17.2 - - + +
115D LEU* 4.9 6.7 - - + -
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Residues in contact with ASN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C MET 2.9 18.6 + - - +
32C LYS* 3.4 10.5 - - - +
33C GLN 3.1 0.6 - - - -
34C LEU* 1.3 76.7 - - - +
36C ILE* 1.3 59.4 + - + +
37C ILE 3.2 0.2 - - - -
38C GLN 3.3 5.2 - - - -
39C ASN* 4.2 1.0 - - - +
40C ALA* 3.2 25.0 + - + +
41C GLU* 4.4 4.3 + - - +
343D ARG* 2.9 52.6 + - - +
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LYS* 3.7 17.7 - - + +
33C GLN* 3.1 19.5 + - - +
34C LEU 3.1 0.4 + - - -
35C ASN* 1.3 80.1 - - + +
37C ILE* 1.3 66.5 + - + +
128D SER* 4.4 4.9 + - - +
129D GLN* 2.9 21.5 + - - -
343D ARG* 3.8 1.0 + - - -
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN 4.2 13.9 - - - +
34C LEU* 3.0 12.9 + - + +
36C ILE* 1.3 86.9 - - + +
38C GLN* 1.3 63.4 - - + +
112D VAL* 4.4 15.0 - - + -
115D LEU* 5.1 5.6 - - + -
116D ARG* 5.4 3.8 - - - +
120D LEU* 3.4 40.2 - - + -
128D SER 4.0 10.5 - - - +
129D GLN* 3.0 15.5 - - - +
130D LEU* 2.9 60.2 + - + +
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.3 43.2 + - + +
35C ASN* 3.3 12.3 - - - -
36C ILE 3.6 0.8 - - - -
37C ILE* 1.3 81.6 - - + +
39C ASN* 1.3 73.4 + - - +
40C ALA* 3.2 2.9 + - - +
103D LEU 5.6 1.9 - - - +
104D GLY* 6.1 0.9 - - - -
111D PHE* 4.3 12.4 - - - -
115D LEU* 5.6 2.4 - - - +
129D GLN* 3.6 7.5 + - - -
130D LEU* 2.8 27.8 + - - +
131D ILE* 3.8 26.2 - - + +
132D THR* 4.7 4.6 + - - +
338D HIS* 6.2 0.7 - - - -
343D ARG* 3.1 18.0 + - - -
344D PRO* 6.5 0.2 - - - -
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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