Contacts of the strand formed by residues 45 - 51 (chain D) in PDB entry 2OQH
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 GLU 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ARG* 4.1 19.2 + - + -
38D VAL 3.4 6.5 - - - +
39D ARG* 3.1 36.1 + - + -
43D GLY 3.4 15.5 - - - +
44D VAL* 1.3 79.1 - - - +
46D GLY* 1.3 57.1 + - - +
47D TRP* 4.3 14.4 + - - +
110D LYS* 2.7 40.3 + - - +
359D GLU* 3.8 17.7 - - - +
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Residues in contact with GLY 46 (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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37D ARG* 3.3 5.2 - - - +
38D VAL 2.8 39.4 + - - -
45D GLU* 1.3 74.8 - - - +
47D TRP* 1.3 62.9 + - - -
103D ALA* 3.2 25.4 - - - +
106D ASP* 3.4 6.1 - - - -
107D ALA* 3.8 11.3 - - - +
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Residues in contact with TRP 47 (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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11D TRP* 3.6 17.0 - + - -
35D VAL* 3.6 19.7 - - + -
36D VAL 3.4 9.9 - - - -
37D ARG* 3.5 30.5 - - + -
45D GLU* 4.1 15.4 + - - +
46D GLY* 1.3 77.3 - - - -
48D GLY* 1.3 59.2 - - - +
102D VAL 3.8 0.3 - - - +
103D ALA* 3.4 13.2 + - - -
106D ASP* 2.8 20.3 + - - +
110D LYS* 4.0 13.5 - - - +
304D ILE* 4.3 10.1 - - + -
353D LEU* 3.5 23.8 - - + +
355D VAL* 5.8 3.4 - - + -
357D VAL* 3.5 48.4 - - + +
359D GLU* 3.8 22.0 - - + -
362D LEU* 3.4 34.5 - - + -
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Residues in contact with GLY 48 (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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34D THR 4.6 0.4 - - - -
35D VAL* 3.5 8.0 - - - +
36D VAL 2.9 33.7 + - - -
47D TRP* 1.3 74.8 - - - +
49D GLU* 1.3 60.1 + - - +
99D ALA* 3.6 23.6 - - - -
102D VAL* 4.2 5.8 - - - -
103D ALA* 3.8 3.7 - - - +
304D ILE* 3.8 7.9 - - - +
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Residues in contact with GLU 49 (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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15D LEU* 6.0 1.8 - - + -
33D ARG* 2.8 39.5 + - + +
34D THR 3.4 8.7 - - - +
35D VAL* 4.9 6.7 - - + -
48D GLY* 1.3 74.2 - - - +
50D THR* 1.3 62.2 + - - +
99D ALA* 4.6 2.9 - - - +
102D VAL* 5.2 2.8 - - - +
272D TYR* 3.2 25.0 - - - -
302D LEU* 2.8 34.7 + - - +
303D GLY 3.8 0.2 + - - -
304D ILE* 3.3 35.2 + - + +
305D ALA* 3.0 29.6 + - - +
333D ASP* 5.3 0.9 - - - +
334D ILE* 6.3 0.2 - - + -
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Residues in contact with THR 50 (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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33D ARG* 3.3 18.3 + - - +
34D THR* 2.8 41.4 + - + -
49D GLU* 1.3 75.0 - - - +
51D MSE 1.3 66.2 + - - +
56D VAL* 3.6 30.1 - - + -
95D ALA* 2.8 33.0 + - - +
99D ALA* 3.6 20.9 - - + -
272D TYR* 3.8 12.9 - - - +
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Residues in contact with MSE 51 (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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88B PHE* 4.3 11.2 - - + -
33D ARG* 3.4 24.1 - - - +
50D THR* 1.3 82.3 + - - +
52D TRP* 1.3 108.2 + - + +
56D VAL* 3.3 17.0 - - + +
91D TYR* 3.6 40.8 - - + -
92D LEU* 3.1 35.9 - - + -
95D ALA* 3.6 18.2 - - + -
272D TYR* 5.3 7.0 - - + +
299D GLY* 5.0 4.9 - - - +
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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