Contacts of the strand formed by residues 109 - 114 (chain E) 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 THR 109 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E GLN* 3.3 27.8 + - - +
9E SER 5.0 0.7 - - - -
10E PRO* 2.9 26.0 + - + +
11E LYS 3.4 5.8 - - - +
13E LEU* 3.8 30.3 - - + -
23E LEU* 4.6 16.8 - - + +
24E SER 5.3 0.9 + - - -
90E PHE* 3.5 5.4 - - - -
91E TYR* 2.8 34.0 + - - +
108E GLY* 1.3 73.0 - - - -
110E ARG* 1.3 68.0 + - - +
111E LEU* 3.7 2.1 + - - +
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Residues in contact with ARG 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLY* 5.4 9.4 - - - +
11E LYS* 2.9 18.5 + - + +
12E TYR* 3.6 19.9 - - + -
13E LEU 2.9 28.1 + - - +
89E ALA 3.9 5.7 + - - -
90E PHE* 3.7 27.0 - - + +
109E THR* 1.3 71.1 - - - +
111E LEU* 1.3 61.0 + - - +
112E THR* 5.4 2.4 + - - -
153E ASP* 3.3 46.1 + - - +
154E HIS* 3.4 20.0 + - - +
176E PRO* 5.9 0.4 - - - +
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU* 3.4 25.4 - - + +
15E ARG* 4.5 7.2 - - + -
21E VAL* 4.2 20.0 - - + -
23E LEU* 4.8 7.6 - - + -
80E VAL* 4.1 24.0 - - + -
87E PRO 3.6 17.9 - - - +
88E THR* 3.2 6.6 - - - +
89E ALA 3.0 29.7 + - - +
91E TYR* 3.8 22.7 - - + -
109E THR* 3.7 2.6 + - + +
110E ARG* 1.3 73.2 - - - +
112E THR* 1.3 75.6 + - - +
113E VAL* 4.1 19.5 - - + -
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Residues in contact with THR 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU 3.0 7.1 + - - +
14E PHE* 3.4 12.2 - - + -
15E ARG 3.0 23.6 + - - -
88E THR* 3.6 18.2 - - + +
110E ARG* 5.4 2.6 + - - -
111E LEU* 1.3 76.6 + - - +
113E VAL* 1.3 64.5 + - - +
151E TYR* 3.5 28.3 - - + +
152E PRO* 3.8 20.5 - - + +
153E ASP 5.1 1.0 + - - -
154E HIS* 3.1 28.8 + - - -
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Residues in contact with VAL 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG* 3.2 13.7 - - + +
16E LYS 4.1 1.8 - - - +
17E GLU* 3.5 36.1 - - + +
18E GLY 5.0 0.9 - - - +
19E GLN 5.9 2.2 - - - +
21E VAL* 5.8 1.6 - - + -
80E VAL* 5.8 0.9 - - + -
87E PRO* 3.7 38.6 - - + -
88E THR* 2.9 14.7 + - - +
111E LEU* 4.1 20.0 - - + -
112E THR* 1.3 77.9 - - - +
114E THR* 1.3 62.1 + - - +
151E TYR* 4.1 5.0 + - - -
184E ASN* 5.6 3.5 + - - -
185E ASP* 4.8 1.9 - - - +
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Residues in contact with THR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E PHE* 3.1 34.1 - - + -
15E ARG 3.0 10.0 + - - +
16E LYS* 3.6 1.5 - - - -
17E GLU* 2.7 34.3 + - - -
112E THR 4.1 0.4 - - - -
113E VAL* 1.3 74.4 - - - +
115E GLU* 1.3 66.0 + - - +
116E ASP 3.5 21.3 + - - +
117E LEU* 4.1 5.2 - - + +
119E ASN* 3.3 18.5 + - - -
120E VAL* 5.0 0.2 - - + -
151E TYR* 3.4 26.3 + - - -
185E ASP* 3.5 4.6 + - - -
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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