Contacts of the strand formed by residues 110 - 115 (chain B) in PDB entry 2OTD
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 MSE 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PRO* 3.3 36.1 - - + +
6B TYR* 3.9 20.2 - - + -
7B PRO* 3.8 20.0 - - + -
36B LYS* 2.9 19.6 + - + +
37B MSE 3.3 9.2 - - - -
38B ILE* 3.0 28.6 + - - +
104B CYS* 4.8 0.4 - - - -
108B GLY 5.6 4.0 - - - +
109B MSE 1.3 78.6 - - - +
111B ALA* 1.3 61.9 + - - +
137B TRP* 5.6 2.7 - - - +
141B THR* 3.9 32.1 - - + +
142B PRO 5.8 0.2 - - - +
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Residues in contact with ALA 111 (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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6B TYR* 4.9 0.5 - - - -
37B MSE 4.0 6.0 - - - +
38B ILE 3.3 3.6 - - - -
40B PHE* 3.7 25.1 - - + -
104B CYS* 4.3 5.8 - - - -
110B MSE 1.3 79.8 - - - +
112B ASN* 1.3 53.3 + - - +
113B ILE* 3.7 1.1 - - + -
137B TRP* 3.8 30.4 - - + +
143B PRO* 3.4 11.8 - - + +
144B LEU* 2.8 31.5 + - - +
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Residues in contact with ASN 112 (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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10B VAL* 4.9 2.5 - - + -
37B MSE 3.7 19.5 - - + +
38B ILE 2.8 9.7 + - - +
39B GLU* 3.2 47.0 - - + +
40B PHE* 3.2 8.8 + - - -
111B ALA* 1.3 71.2 - - - +
113B ILE* 1.3 57.2 + - - +
114B GLU* 3.2 4.2 + - - +
144B LEU* 2.6 26.7 + - + +
146B SER* 2.5 33.1 + - - +
168B LEU* 5.2 0.2 - - - +
189B HIS* 4.3 14.0 + - - -
211B LEU* 4.3 9.5 - - + +
301B PO4 4.7 4.9 + - - -
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Residues in contact with ILE 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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40B PHE* 3.8 24.2 - - + -
42B ALA* 3.7 28.3 - - + -
97B LEU* 4.0 10.3 - - + -
111B ALA* 3.7 2.0 - - + -
112B ASN* 1.3 68.7 - - - +
114B GLU* 1.3 60.9 + - - +
115B ILE* 3.1 5.0 + - - +
129B VAL* 4.0 17.0 - - + -
133B ALA* 4.0 21.3 - - + -
137B TRP* 3.9 27.8 - - + -
143B PRO* 4.1 18.8 - - + -
144B LEU 3.0 8.7 + - - +
145B LEU* 3.6 11.3 - - + -
146B SER 3.3 13.3 + - - -
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Residues in contact with GLU 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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39B GLU* 3.5 16.4 - - + +
40B PHE 3.1 7.4 + - - +
41B ASP* 3.4 13.8 - - - +
42B ALA 3.0 25.3 + - - -
54B HIS* 5.0 3.3 + - - -
112B ASN* 3.2 6.6 + - - +
113B ILE* 1.3 69.5 - - - +
115B ILE* 1.3 70.4 + - - +
116B LYS* 3.4 19.8 + - + +
146B SER* 4.0 14.4 - - - +
147B SER* 4.5 7.4 - - - -
148B PHE* 3.4 25.9 - - - -
168B LEU* 4.5 3.8 - - + -
301B PO4 2.7 42.4 + - - +
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Residues in contact with ILE 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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42B ALA* 4.0 4.3 - - - +
113B ILE 3.9 8.3 - - - +
114B GLU* 1.3 71.4 - - - +
116B LYS* 1.3 58.8 + - - +
117B PRO* 3.7 4.4 - - + +
125B THR* 3.4 35.9 - - + -
126B GLY* 4.1 18.8 - - - +
129B VAL* 3.9 31.2 - - + -
145B LEU* 4.6 17.9 - - + -
146B SER 3.0 18.2 + - - +
147B SER* 3.1 31.9 + - - -
148B PHE* 4.3 2.1 + - - -
149B GLU* 5.0 0.3 - - - +
152B ALA* 4.1 17.0 - - + -
153B LEU* 5.3 1.3 - - + +
156B ALA* 4.8 7.6 - - + -
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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