Contacts of the helix formed by residues 24 - 38 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B THR* 3.6 1.8 + - - -
21B GLU 3.2 15.1 + - - -
22B VAL* 3.8 1.4 - - - +
23B PRO* 1.3 73.5 - - - +
25B PRO* 1.3 72.1 - - - +
27B SER* 3.2 4.1 + - - -
28B ARG* 2.9 33.4 + - - +
59B ASP* 5.0 2.2 + - - -
61B ASP* 3.1 20.5 + - - +
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 4.2 17.0 - - + +
24B GLY* 1.3 85.2 - - - +
26B ARG* 1.3 55.6 + - - +
28B ARG* 3.3 28.2 + - - +
29B GLU* 3.0 28.1 + - - +
61B ASP* 3.2 14.1 - - - +
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 5.9 1.6 - - - +
25B PRO* 1.3 73.2 - - - +
27B SER* 1.3 63.0 + - - +
29B GLU* 3.3 7.5 + - - +
30B LEU* 3.0 29.7 + - + +
60B VAL* 3.8 27.4 - - + +
61B ASP* 2.8 20.9 + - - +
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 3.8 19.7 - - - -
24B GLY 3.2 10.5 + - - -
26B ARG* 1.3 76.8 - - - +
28B ARG* 1.3 51.5 + - - +
30B LEU* 3.2 2.1 + - - +
31B MET* 2.8 40.3 + - - +
45B PHE* 3.4 8.4 - - - +
46B PHE* 3.1 31.8 + - - +
59B ASP* 4.7 2.4 + - - +
60B VAL* 3.2 17.0 + - - +
61B ASP* 3.2 10.1 + - - -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 5.1 4.2 + - - +
23B PRO* 2.9 42.5 + - + +
24B GLY* 2.9 25.5 + - - +
25B PRO* 3.3 30.9 + - + +
27B SER* 1.3 74.4 - - - +
29B GLU* 1.3 60.9 - - - +
31B MET* 3.7 9.3 - - - +
32B LYS* 3.0 24.1 + - - +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO 3.0 14.2 + - - +
26B ARG* 3.5 12.1 - - - +
28B ARG* 1.3 77.1 - - - +
30B LEU* 1.3 62.8 + - + +
32B LYS* 3.2 13.2 + - - +
33B GLN* 2.5 53.1 + - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 4.0 36.1 - - + +
112A VAL* 4.3 6.0 - - + +
26B ARG* 3.0 22.7 + - + +
29B GLU* 1.3 74.6 - - + +
31B MET* 1.3 59.3 + - - +
33B GLN* 3.2 27.6 + - - +
34B LEU* 2.9 30.7 + - - +
46B PHE* 3.5 49.1 - - + -
60B VAL* 4.2 8.3 - - + -
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Residues in contact with MET 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 3.9 25.1 - - + -
27B SER* 2.8 34.9 + - - +
28B ARG* 3.7 9.4 - - + +
29B GLU 3.3 0.2 - - - -
30B LEU* 1.3 73.2 - - - +
32B LYS* 1.3 56.6 + - - +
34B LEU* 3.8 2.8 - - - +
35B ASN* 2.9 31.1 + - - +
40B ALA* 4.2 10.1 - - + +
43B VAL* 3.3 41.3 - - + +
44B HIS 4.0 9.2 - - - +
45B PHE* 4.4 0.4 - - - -
46B PHE* 3.6 19.1 - - + -
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG 3.0 14.4 + - - +
29B GLU* 3.2 18.1 + - - +
31B MET* 1.3 73.5 - - - +
33B GLN* 1.3 68.4 + - + +
35B ASN* 3.3 15.4 + - - +
36B ILE* 3.4 20.2 + - + +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 4.2 9.7 - - + +
116A ARG* 3.3 37.9 + - - +
29B GLU* 2.5 42.7 + - - +
30B LEU* 3.5 27.9 - - - +
32B LYS* 1.3 80.5 - - + +
34B LEU* 1.3 62.9 + - - +
36B ILE* 3.1 26.8 + - - +
37B ILE* 4.0 8.0 - - - +
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU 5.6 1.8 - - - +
107A PRO* 4.5 2.7 - - + -
111A PHE* 4.1 27.8 - - + -
112A VAL* 3.9 16.3 - - + +
115A LEU* 4.9 4.5 - - + -
30B LEU 2.9 16.5 + - - +
31B MET* 3.8 4.5 - - - +
33B GLN* 1.3 74.9 - - - +
35B ASN* 1.3 58.0 + - - +
37B ILE* 2.9 29.8 + - + -
38B GLN* 3.2 44.8 + - + +
40B ALA* 4.1 4.9 - - + -
43B VAL* 4.1 23.1 - - + -
46B PHE* 3.8 20.6 - - + -
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Residues in contact with ASN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG* 2.8 46.2 + - - +
31B MET 2.9 19.5 + - - +
32B LYS* 3.5 9.6 - - - +
33B GLN 3.2 0.4 - - - -
34B LEU* 1.3 75.7 - - - +
36B ILE* 1.3 60.0 + - + +
38B GLN 3.2 5.8 - - - -
39B ASN* 4.1 0.9 - - - +
40B ALA* 3.1 30.6 + - + +
41B GLU* 4.3 5.0 + - - +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A SER* 4.6 4.0 + - - +
129A GLN* 3.1 21.0 + - - -
343A ARG* 3.7 2.3 + - - -
32B LYS* 3.4 16.7 + - + +
33B GLN* 3.1 18.4 + - - +
34B LEU 3.1 0.8 + - - -
35B ASN* 1.3 80.0 - - + +
37B ILE* 1.3 67.5 + - + +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 4.3 16.6 - - + -
115A LEU* 5.1 5.6 - - + -
116A ARG* 5.3 4.9 - - - +
120A LEU* 3.6 37.0 - - + -
128A SER 4.0 10.8 - - - +
129A GLN* 3.2 11.3 - - - +
130A LEU* 2.9 52.3 + - + +
33B GLN 4.0 13.9 - - - +
34B LEU* 2.9 13.9 + - + +
36B ILE* 1.3 86.0 - - + +
38B GLN* 1.3 63.6 + - + +
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU 5.5 1.7 - - - +
104A GLY* 6.1 0.7 - - - -
111A PHE* 4.3 12.8 - - - -
115A LEU* 5.6 2.6 - - - +
129A GLN* 3.6 8.3 + - - -
130A LEU* 2.8 28.0 + - - +
131A ILE* 3.9 24.9 - - + +
132A THR* 4.7 4.9 + - - +
338A HIS* 6.2 0.7 - - - -
343A ARG* 3.0 17.8 + - - -
34B LEU* 3.2 44.3 + - + +
35B ASN* 3.1 14.9 - - - +
36B ILE 3.5 1.4 - - - -
37B ILE* 1.3 81.4 - - + +
39B ASN* 1.3 74.7 + - - +
40B ALA* 5.3 0.7 - - - +
43B VAL* 5.8 0.3 - - - +
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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