Contacts of the helix formed by residues 24 - 38 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D THR* 3.6 1.3 + - - -
21D GLU 3.1 16.1 + - - -
22D VAL* 3.8 1.4 - - - +
23D PRO* 1.3 73.8 - - - +
25D PRO* 1.3 72.3 - - - +
27D SER* 3.2 3.7 + - - -
28D ARG* 2.9 32.9 + - - +
59D ASP* 4.9 2.0 + - - -
61D ASP* 3.1 21.0 + - - +
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Residues in contact with PRO 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D THR* 4.2 17.5 - - + +
24D GLY* 1.3 82.7 - - - +
26D ARG* 1.3 56.4 + - - +
28D ARG* 3.3 27.6 + - - +
29D GLU* 3.0 28.1 + - - +
61D ASP* 3.2 13.0 - - - +
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLU* 6.0 0.9 - - - +
25D PRO* 1.3 71.5 - - - +
27D SER* 1.3 64.3 + - - +
29D GLU* 3.3 7.6 + - - +
30D LEU* 3.0 29.7 + - + +
60D VAL* 3.8 26.5 - - + +
61D ASP* 2.8 21.9 + - - +
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Residues in contact with SER 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PRO* 3.8 20.0 - - - -
24D GLY 3.2 8.6 + - - -
26D ARG* 1.3 76.3 - - - +
28D ARG* 1.3 51.5 + - - +
30D LEU* 3.2 2.3 + - - +
31D MET* 2.8 41.6 + - - +
45D PHE* 3.4 7.3 - - - +
46D PHE* 3.0 32.0 + - - -
59D ASP* 4.7 2.3 + - - +
60D VAL* 3.2 17.2 + - - +
61D ASP* 3.1 11.2 + - - -
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLU* 5.0 4.8 + - - +
23D PRO* 2.9 42.1 + - + +
24D GLY* 2.9 25.5 + - - +
25D PRO* 3.3 31.3 + - - +
27D SER* 1.3 74.6 - - - +
29D GLU* 1.3 58.2 + - - +
31D MET* 3.4 10.0 + - + +
32D LYS* 3.0 28.9 + - - +
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PRO 3.0 14.3 + - - +
26D ARG* 3.5 11.2 - - - +
27D SER 3.2 0.2 - - - -
28D ARG* 1.3 76.8 - - - +
30D LEU* 1.3 64.4 + - + +
32D LYS* 3.3 13.8 + - - +
33D GLN* 2.5 53.4 + - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLU* 4.0 27.4 - - + +
112C VAL* 4.4 6.8 - - + +
26D ARG* 3.0 22.9 + - + +
27D SER 3.7 0.2 - - - +
29D GLU* 1.3 73.5 - - + +
31D MET* 1.3 59.9 + - - +
33D GLN* 3.2 28.4 + - - +
34D LEU 2.9 25.1 + - - -
46D PHE* 3.5 53.0 - - + -
60D VAL* 4.2 15.0 - - + -
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Residues in contact with MET 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 3.9 26.2 - - + -
27D SER* 2.8 35.1 + - - +
28D ARG* 3.6 9.4 - - + +
29D GLU 3.3 0.2 - - - -
30D LEU* 1.3 73.4 - - - +
32D LYS* 1.3 56.5 + - - +
34D LEU* 3.9 3.2 - - - +
35D ASN* 3.0 30.2 + - - +
40D ALA* 4.2 10.9 - - + +
43D VAL* 3.4 40.2 - - + +
44D HIS 4.1 8.1 - - - +
45D PHE* 4.4 0.7 - - - -
46D PHE* 3.6 18.8 - - + -
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Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG 3.0 14.6 + - - +
29D GLU* 3.5 18.2 - - - +
30D LEU 3.2 0.2 - - - -
31D MET* 1.3 77.5 - - - +
33D GLN* 1.3 63.9 + - + +
35D ASN* 3.2 18.7 + - - +
36D ILE* 3.5 16.3 + - + +
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Residues in contact with GLN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C VAL* 4.1 10.9 - - + +
116C ARG* 3.3 37.5 + - - +
29D GLU* 2.5 40.7 + - - +
30D LEU* 3.2 27.4 + - - +
32D LYS* 1.3 79.7 - - + +
34D LEU* 1.3 62.4 + - - +
36D ILE* 3.2 25.8 + - - +
37D ILE* 4.1 7.4 + - - +
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU 5.6 1.3 - - - +
107C PRO* 4.6 3.1 - - + -
111C PHE* 4.0 27.4 - - + -
112C VAL* 3.9 18.3 - - + +
115C LEU* 4.7 5.2 - - + -
30D LEU 2.9 15.8 + - - +
31D MET 4.0 3.6 - - - +
33D GLN* 1.3 76.6 - - - +
35D ASN* 1.3 56.7 + - - +
37D ILE* 3.0 29.4 + - + +
38D GLN* 3.2 47.9 + - + +
40D ALA* 4.3 5.2 - - + -
43D VAL* 4.2 21.3 - - + -
46D PHE* 4.0 18.8 - - + -
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Residues in contact with ASN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C ARG* 2.7 61.8 + - - +
31D MET 3.0 19.1 + - - +
32D LYS* 3.5 10.5 - - - +
33D GLN 3.2 0.4 - - - -
34D LEU* 1.3 73.9 - - - +
36D ILE* 1.3 57.9 + - + +
37D ILE 3.2 0.2 - - - -
38D GLN 3.1 5.1 - - - +
39D ASN* 4.2 1.0 - - - +
40D ALA* 3.4 22.9 + - + +
41D GLU* 4.7 4.7 + - - +
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C SER* 4.5 5.1 + - - +
129C GLN* 2.9 21.3 + - - -
343C ARG* 3.7 1.8 + - - +
32D LYS* 3.5 14.6 + - + +
33D GLN* 3.4 16.8 - - - +
34D LEU 3.2 0.6 - - - -
35D ASN* 1.3 80.0 - - + +
37D ILE* 1.3 68.4 + - + +
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Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C VAL* 4.4 16.4 - - + -
115C LEU* 5.1 5.6 - - + -
116C ARG* 5.4 4.3 - - - +
120C LEU* 3.3 36.3 - - + -
128C SER 4.0 14.1 - - - +
129C GLN* 3.2 12.7 - - - +
130C LEU* 2.9 57.9 + - + +
33D GLN 4.3 11.9 - - - +
34D LEU* 3.0 16.1 + - + +
36D ILE* 1.3 86.6 - - + +
38D GLN* 1.3 62.9 + - + +
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU 5.5 2.4 - - - +
104C GLY* 6.0 1.4 - - - -
111C PHE* 4.4 11.4 - - - -
115C LEU* 5.6 2.6 - - - +
129C GLN* 3.6 8.7 + - - -
130C LEU 2.8 27.6 + - - +
131C ILE* 3.9 25.2 - - + +
132C THR* 4.7 4.9 + - - +
338C HIS* 6.1 0.7 - - - -
343C ARG* 3.1 17.2 + - - -
344C PRO* 6.4 0.2 - - - -
34D LEU* 3.2 44.0 + - + +
35D ASN* 3.1 12.1 - - - +
36D ILE 3.6 0.8 - - - -
37D ILE* 1.3 79.9 - - - +
39D ASN* 1.3 74.0 + - - +
40D ALA* 3.2 3.3 + - - -
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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