Contacts of the strand formed by residues 112 - 117 (chain B) in PDB entry 2EYT
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 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 3.8 10.9 + - - +
7B THR 4.4 4.2 + - - -
8B PRO* 2.7 31.8 + - + +
9B ARG 3.5 5.8 - - - +
11B LEU* 4.7 6.1 - - + -
21B LEU* 3.8 41.5 - - + +
22B GLU 5.4 0.2 + - - -
34B TRP* 5.0 0.2 - - - -
88B SER 3.7 0.2 - - - +
89B GLN* 3.2 6.7 - - - +
90B TYR* 2.9 34.9 + - - -
111B GLY* 1.3 73.8 - - - -
113B ARG* 1.3 70.3 + - - +
114B LEU* 3.6 5.0 + - + +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG 2.9 13.9 + - - +
10B TYR* 3.6 20.7 - - + -
11B LEU 3.2 22.9 + - - -
39B PRO* 4.6 20.3 - - - +
88B SER 3.5 8.5 - - - +
89B GLN* 4.3 9.9 - - + +
111B GLY 4.1 0.6 - - - -
112B THR* 1.3 73.1 - - - +
114B LEU* 1.3 60.7 + - - +
115B THR* 5.1 1.4 + - - +
156B ASP* 3.0 47.9 + - - +
157B HIS* 3.2 30.2 + - + -
179B PRO* 6.2 0.8 - - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.5 40.2 - - + +
13B ILE* 4.1 19.5 - - + -
19B ILE* 4.2 6.7 - - + -
21B LEU* 5.4 2.7 - - + -
79B LEU* 3.7 11.9 - - + -
86B HIS* 3.2 40.8 - - + +
87B THR* 3.1 2.8 - - - +
88B SER 2.7 39.4 + - - +
90B TYR* 3.7 19.7 - - + -
112B THR* 3.6 6.6 + - + -
113B ARG* 1.3 75.2 - - - +
115B THR* 1.3 64.4 + - - +
116B VAL* 3.8 6.7 - - + -
157B HIS* 4.6 0.2 - - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU 3.0 9.0 + - - +
12B VAL* 3.5 7.0 - - + +
13B ILE* 3.1 25.1 + - - +
87B THR* 3.5 17.4 - - + +
113B ARG* 5.1 1.6 + - - +
114B LEU* 1.3 75.9 + - - +
116B VAL* 1.3 71.0 + - - +
154B TYR* 3.6 27.4 - - + +
155B PRO* 3.9 19.0 - - + +
156B ASP* 5.2 0.9 + - - +
157B HIS* 3.1 27.5 + - - -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.4 20.6 - - + +
14B GLY 4.3 1.8 - - - +
15B THR* 4.1 9.9 - - - +
19B ILE* 4.7 0.4 - - + -
82B ALA* 4.0 9.9 - - + -
83B ARG* 3.4 34.1 - - - +
84B PRO* 3.6 17.6 - - + +
86B HIS* 3.6 32.1 - - + -
87B THR* 2.8 17.9 + - - +
114B LEU* 3.8 11.2 - - + -
115B THR* 1.3 81.1 - - - +
117B THR* 1.3 62.7 + - - +
154B TYR* 4.7 1.6 + - - -
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 4.1 16.6 - - + -
13B ILE 3.1 12.7 + - - +
14B GLY* 3.3 1.9 - - - -
15B THR* 3.3 18.5 + - - -
84B PRO* 6.0 1.6 - - - -
115B THR* 4.8 0.7 - - - -
116B VAL* 1.3 77.5 - - - +
118B GLU* 1.3 67.2 + - - +
119B ASP 3.3 15.9 + - - +
120B LEU* 4.0 22.7 - - + -
123B VAL* 4.8 1.1 - - + -
154B TYR* 3.7 19.5 - - + -
188B ASP* 2.4 31.4 + - - -
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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