Contacts of the strand formed by residues 33 - 38 (chain D) in PDB entry 1OGA
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 LEU 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.6 12.6 - - + -
24D CYS* 4.4 15.3 - - - -
30D PHE* 5.0 8.5 - - + -
32D SER* 1.3 77.0 - - - +
34D GLN* 1.3 72.8 + - - +
35D TRP* 3.7 17.7 - - + +
48D VAL* 4.0 0.3 - - - +
49D THR* 3.3 3.5 - - - -
50D VAL* 2.8 47.0 + - + +
66D PHE* 4.1 18.2 - - + -
71D LYS 6.0 0.2 - - - -
72D ASP* 4.9 2.9 - - - +
73D SER* 3.6 38.8 - - - +
90D CYS* 4.7 1.6 - - + -
91D ALA 3.3 17.0 - - - +
92D GLY* 5.0 0.4 - - - -
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Residues in contact with GLN 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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32D SER* 4.3 9.8 + - - +
33D LEU* 1.3 88.5 + - - +
35D TRP* 1.3 64.7 + - - +
36D TYR* 3.6 22.9 - - + +
46D LEU* 3.7 9.2 - - + -
48D VAL 3.2 5.6 - - - +
49D THR* 3.0 39.0 + - - +
90D CYS* 3.2 4.5 - - - -
91D ALA* 2.8 39.1 + - + +
93D ALA 4.8 0.2 + - - -
99D LEU* 3.4 26.2 - - - +
100E SER 4.9 0.3 - - - +
101E TYR* 4.5 0.8 - - - -
102E GLU* 3.6 33.6 - - + +
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Residues in contact with TRP 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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7D GLN* 3.7 23.3 - - - -
22D VAL* 3.9 32.5 - - + -
23D TYR 4.4 2.5 - - - -
24D CYS* 3.6 31.0 - - + -
33D LEU* 3.7 14.6 - - + +
34D GLN* 1.3 72.3 - - - +
36D TYR* 1.3 58.7 + - - +
46D LEU* 3.7 5.5 - - - +
47D LEU* 2.8 33.3 + - + +
48D VAL* 3.1 17.0 + - + -
50D VAL* 5.6 1.3 - - + -
64D PHE* 3.5 36.8 - + + -
73D SER* 2.9 19.9 + - - -
74D SER* 3.9 21.4 + - - -
75D LEU* 4.1 13.7 - - + -
88D TYR* 4.6 9.9 - + + -
89D LEU 3.3 20.0 - - - -
90D CYS* 3.9 7.4 - - + -
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Residues in contact with TYR 36 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D GLN* 3.6 22.0 - - + +
35D TRP* 1.3 75.7 - - - +
37D ARG* 1.3 60.6 + - - +
44D PRO* 4.0 24.5 - - + -
45D VAL 3.2 8.1 - - - +
46D LEU* 3.5 35.0 - - + +
47D LEU* 3.9 4.5 - - - -
88D TYR* 3.3 8.5 - - - +
89D LEU* 2.8 44.1 + - + +
91D ALA* 4.3 4.5 - - + -
99D LEU* 3.8 3.9 - - + +
101D PHE* 4.0 27.6 - + - -
103E GLN* 2.7 50.6 + - - +
104E TYR* 5.4 0.2 - - - -
105E PHE* 3.7 17.0 - + - -
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Residues in contact with ARG 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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36D TYR* 1.3 73.9 - - - +
38D GLN* 1.3 63.0 + - - +
39D GLU* 3.8 26.0 + - - +
44D PRO* 4.4 0.4 - - - -
45D VAL* 2.8 59.4 + - - +
47D LEU* 3.6 27.4 - - + +
62D LEU* 5.1 6.9 - - - +
83D GLY 4.8 7.5 + - - -
84D ASP* 4.3 5.8 + - - +
85D THR 4.5 0.2 - - - -
86D GLY* 4.6 2.7 - - - -
87D LEU 3.3 4.5 - - - +
88D TYR* 3.4 44.1 + - + -
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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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37D ARG* 1.3 76.1 - - - +
39D GLU* 1.3 77.6 + - - +
40D PRO* 4.6 2.0 - - - +
41D GLY 5.0 1.6 - - - +
42D GLU 3.0 24.7 + - - +
43D GLY 4.9 1.1 - - - -
44D PRO* 3.9 24.8 - - + +
86D GLY* 3.7 2.9 - - - -
87D LEU* 2.7 59.9 + - + +
89D LEU* 4.7 6.0 - - + +
39E GLN* 2.8 44.5 + - - -
45E LEU* 5.3 0.4 - - - -
90E PHE* 4.0 2.8 - - - -
92E LEU* 3.9 12.7 - - - +
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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