Contacts of the helix formed by residues 24 - 38 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 3.6 1.5 + - - -
21A GLU 3.2 17.1 + - - -
22A VAL* 3.7 1.8 - - - +
23A PRO* 1.3 72.9 - - - +
25A PRO* 1.3 72.4 - - - +
27A SER* 3.1 3.9 + - - -
28A ARG* 2.9 33.4 + - - +
59A ASP* 5.0 1.8 + - - -
61A ASP* 3.1 20.0 + - - +
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Residues in contact with PRO 25 (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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20A THR* 4.3 17.9 - - + +
24A GLY* 1.3 83.1 - - - +
26A ARG* 1.3 54.7 + - - +
28A ARG* 3.3 28.2 + - - +
29A GLU* 3.0 28.5 + - - +
61A ASP* 3.2 13.7 - - - +
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Residues in contact with ARG 26 (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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25A PRO* 1.3 70.8 - - - +
27A SER* 1.3 64.0 + - - +
29A GLU* 3.3 7.7 + - - +
30A LEU* 3.0 29.8 + - + +
60A VAL* 3.7 26.2 - - + +
61A ASP* 2.8 20.9 + - - +
109B GLU* 5.8 1.6 - - - +
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Residues in contact with SER 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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23A PRO* 3.8 18.8 - - - -
24A GLY 3.1 11.0 + - - -
26A ARG* 1.3 76.8 - - - +
28A ARG* 1.3 52.2 + - - +
30A LEU* 3.2 1.9 + - - +
31A MET* 2.8 40.7 + - - +
45A PHE* 3.5 7.6 - - - +
46A PHE* 3.0 32.8 + - - -
59A ASP* 4.7 1.9 + - - +
60A VAL* 3.2 16.9 + - - +
61A ASP* 3.1 9.9 + - - -
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Residues in contact with ARG 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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21A GLU* 5.1 6.5 + - - +
23A PRO* 2.9 42.9 + - + +
24A GLY* 2.9 26.7 + - - +
25A PRO* 3.6 30.3 - - - +
27A SER* 1.3 74.0 - - - +
29A GLU* 1.3 57.0 + - - +
31A MET* 3.4 9.4 + - + +
32A LYS* 3.0 28.1 + - - +
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Residues in contact with GLU 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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25A PRO 3.0 14.2 + - - +
26A ARG* 3.5 11.4 - - - +
28A ARG* 1.3 76.8 - - - +
30A LEU* 1.3 65.0 + - + +
32A LYS* 3.3 13.3 + - - +
33A GLN* 2.4 52.6 + - - +
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Residues in contact with LEU 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 ARG* 3.0 23.0 + - + +
27A SER 3.2 0.2 + - - -
29A GLU* 1.3 74.8 - - + +
31A MET* 1.3 59.9 + - - +
33A GLN* 3.2 29.2 + - - +
34A LEU* 2.9 24.6 + - - +
46A PHE* 3.5 47.9 - - + -
60A VAL* 4.2 8.1 - - + -
109B GLU* 3.9 40.2 - - + +
112B VAL* 4.2 6.5 - - + +
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Residues in contact with MET 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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23A PRO* 3.8 26.5 - - + -
27A SER* 2.8 33.2 + - - +
28A ARG* 3.6 9.9 - - + +
30A LEU* 1.3 77.2 - - - +
32A LYS* 1.3 57.1 + - - +
34A LEU* 3.4 3.3 + - - +
35A ASN* 3.0 30.2 + - - +
40A ALA* 4.2 10.3 - - + +
41A GLU 5.9 0.2 - - - +
43A VAL* 3.3 41.1 - - + +
44A HIS 4.1 8.3 - - - +
45A PHE* 4.4 0.7 - - - -
46A PHE* 3.6 18.8 - - + -
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Residues in contact with LYS 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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28A ARG 3.0 14.9 + - - +
29A GLU* 3.5 17.5 - - - +
30A LEU 3.2 0.2 - - - -
31A MET* 1.3 75.7 - - - +
33A GLN* 1.3 65.6 + - + +
35A ASN* 3.2 15.4 + - - +
36A ILE* 3.5 18.9 + - + +
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Residues in contact with GLN 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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29A GLU* 2.4 44.6 + - - +
30A LEU* 3.2 28.2 + - - +
32A LYS* 1.3 79.8 - - + +
34A LEU* 1.3 62.5 + - - +
36A ILE* 3.3 25.3 + - - +
37A ILE* 4.1 8.5 - - - +
112B VAL* 4.2 9.5 - - + +
116B ARG* 3.3 38.1 + - - +
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Residues in contact with LEU 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 LEU 2.9 16.1 + - - +
31A MET* 3.8 4.7 - - - +
33A GLN* 1.3 76.9 - - - +
35A ASN* 1.3 57.2 + - - +
37A ILE* 3.1 26.3 + - + -
38A GLN* 3.2 46.2 + - + +
40A ALA* 4.1 5.4 - - + -
43A VAL* 4.2 21.3 - - + -
46A PHE* 3.6 22.4 - - + -
103B LEU 5.7 1.3 - - - +
107B PRO* 4.4 2.7 - - + -
111B PHE* 4.0 23.3 - - + -
112B VAL* 3.8 19.2 - - + +
115B LEU* 4.8 4.7 - - + -
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Residues in contact with ASN 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 MET 3.0 17.8 + - - +
32A LYS* 3.5 9.9 - - - +
33A GLN 3.2 0.6 - - - -
34A LEU* 1.3 75.8 - - - +
36A ILE* 1.3 60.8 + - - +
38A GLN 3.2 4.9 - - - -
39A ASN* 5.0 0.3 - - - +
40A ALA* 3.5 20.4 + - + +
41A GLU* 4.7 5.7 + - - +
343B ARG* 2.9 53.4 + - - +
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Residues in contact with ILE 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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32A LYS* 3.7 14.4 - - + +
33A GLN* 3.4 18.2 - - - +
34A LEU 3.2 0.4 - - - -
35A ASN* 1.3 83.3 - - - +
37A ILE* 1.3 67.0 + - + +
128B SER* 4.3 5.1 + - - +
129B GLN* 3.0 20.8 + - - -
343B ARG* 4.0 1.0 + - - -
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Residues in contact with ILE 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 GLN 4.1 13.7 - - - +
34A LEU* 3.1 13.5 + - + +
36A ILE* 1.3 86.8 - - + +
38A GLN* 1.3 67.0 + - + +
112B VAL* 4.3 15.7 - - + -
115B LEU* 5.0 5.8 - - + -
116B ARG* 5.3 5.4 - - - +
120B LEU* 3.3 40.6 - - + -
128B SER 4.0 11.2 - - - +
129B GLN* 3.1 11.3 - - - +
130B LEU* 2.9 58.4 + - + +
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Residues in contact with GLN 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 LEU* 3.2 43.3 + - + +
35A ASN* 3.0 21.3 - - - +
36A ILE 3.5 1.2 - - - -
37A ILE* 1.3 81.2 - - + +
39A ASN* 1.3 74.6 + - - +
40A ALA* 3.2 3.5 + - - +
43A VAL* 5.8 0.7 - - - +
103B LEU 5.6 1.7 - - - +
111B PHE* 4.2 13.9 - - - -
115B LEU* 5.4 2.6 - - - +
129B GLN* 3.6 8.9 + - - -
130B LEU* 2.8 29.2 + - - +
131B ILE* 3.9 23.2 - - + +
132B THR* 4.7 4.4 + - - +
338B HIS* 6.2 0.9 - - - -
343B ARG* 3.1 7.0 + - - -
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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