Contacts of the strand formed by residues 113 - 118 (chain B) in PDB entry 1OIZ
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 LYS 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B VAL* 3.6 29.8 - - + -
104B LEU 4.2 9.9 + - - +
105B ARG 4.7 8.3 + - - -
106B SER 5.5 2.2 - - - +
107B ARG* 3.7 21.7 - - + +
111B GLY 3.7 2.0 + - - -
112B SER* 1.3 73.3 - - - +
114B VAL* 1.3 61.5 + - - +
115B LEU* 4.2 6.1 - - + -
143B ILE* 4.6 13.0 - - + -
146B GLU* 2.7 33.7 + - - +
149B THR* 3.7 17.5 - - + +
153B GLY 3.1 6.9 + - - -
154B ILE* 3.2 19.4 - - + +
155B LYS 2.9 25.3 + - - +
259B TRP* 5.7 3.8 - - - -
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Residues in contact with VAL 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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103B VAL* 3.5 4.4 - - - +
104B LEU* 2.9 56.7 + - + +
106B SER 4.5 5.6 + - - +
108B ASP* 4.1 10.3 - - + +
112B SER 3.8 10.8 - - - +
113B LYS* 1.3 80.1 - - - +
115B LEU* 1.3 67.4 + - - +
116B ILE* 4.6 0.2 - - + -
155B LYS* 3.3 9.2 - - + +
157B ILE* 3.9 25.6 - - + -
237B PHE* 3.9 29.6 - - + -
240B ILE* 4.1 10.1 - - + -
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Residues in contact with LEU 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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101B HIS* 4.2 3.1 - - - +
102B GLY 3.8 3.1 - - - -
103B VAL* 4.1 21.3 - - + -
113B LYS* 4.2 6.7 - - + +
114B VAL* 1.3 84.9 - - - +
116B ILE* 1.3 67.6 + - - +
117B TYR* 3.6 14.8 - - + +
139B THR* 3.8 15.9 - - + -
143B ILE* 3.7 27.4 - - + -
154B ILE* 4.4 4.7 - - + -
155B LYS 2.8 13.7 + - - +
156B ALA* 3.3 3.0 - - - +
157B ILE* 2.7 27.5 + - - +
1277B TRT 3.2 39.7 - - + -
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Residues in contact with ILE 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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100B TYR 4.6 0.2 - - - -
101B HIS* 3.0 21.1 - - - -
102B GLY 2.9 21.2 + - - +
104B LEU* 3.7 33.9 - - + -
114B VAL* 4.6 2.7 - - + -
115B LEU* 1.3 80.4 - - - +
117B TYR* 1.3 70.0 + - - +
118B ARG* 4.3 7.9 - - + -
157B ILE* 3.4 34.5 - - + +
159B ASP* 5.4 0.7 - - + -
241B LEU* 4.5 1.6 - - + -
242B PRO* 4.4 3.4 - - + -
245B TYR* 4.0 31.0 - - + +
252B MET* 3.8 29.6 - - + +
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Residues in contact with TYR 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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100B TYR* 3.3 38.6 - + + +
101B HIS* 3.3 30.9 + + - -
115B LEU* 3.6 17.5 - - + +
116B ILE* 1.3 77.1 - - - +
118B ARG* 1.3 62.5 + - - +
119B ILE* 4.0 1.7 + - + +
136B SER* 2.7 26.3 + - - -
156B ALA* 4.1 5.6 - - + -
157B ILE 2.9 11.2 + - - +
158B PHE* 3.4 45.0 - + + -
159B ASP* 2.9 29.5 + - - +
1277B TRT 2.2 42.2 - - + +
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Residues in contact with ARG 118 (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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98B ALA 4.9 0.2 + - - -
99B GLY* 3.0 30.3 + - - +
100B TYR* 2.7 29.2 + - - +
116B ILE* 4.3 7.9 - - + -
117B TYR* 1.3 76.0 - - - +
119B ILE* 1.3 66.5 + - - +
120B ALA* 3.2 3.6 - - + +
121B HIS* 3.0 40.7 + - + +
159B ASP* 3.8 9.4 - - + +
244B GLU* 5.2 5.9 - - - +
245B TYR* 3.3 27.0 + - - +
252B MET* 3.7 31.0 - - + +
253B GLU* 2.9 43.4 + - - -
256B CYS* 3.6 10.9 - - - -
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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