Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 5OA3
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 PHE 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.9 27.4 - + - -
82B ARG* 5.3 4.3 - - - -
105B LEU* 4.2 20.2 - - + -
109B LYS* 4.1 18.8 - - - -
113B MET* 4.0 24.0 - - + -
139B CYS* 3.5 11.9 - - - -
140B VAL* 3.2 27.6 + - + +
191B ASP* 3.7 14.8 - - + +
194B GLY* 4.9 2.5 - - - -
197B ILE* 6.3 0.2 - - - -
209B ASP* 3.4 31.9 - - + -
210B VAL* 1.3 86.4 - - - +
212B VAL* 1.3 71.0 + - - +
213B ARG* 3.6 3.6 - - + +
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Residues in contact with VAL 212 (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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82B ARG* 3.7 8.5 + - - +
103B MET* 3.2 22.5 - - + +
105B LEU* 4.0 7.3 - - - +
137B LEU* 4.9 11.4 - - + -
138B PHE 3.2 19.1 - - - +
172B MET* 3.6 24.5 - - + -
188B LEU* 3.6 31.0 - - + -
191B ASP* 3.6 21.8 + - - +
193B ILE* 5.0 9.4 - - + -
211B PHE* 1.3 72.7 - - - +
213B ARG* 1.3 60.3 + - - +
214B LYS 3.3 6.1 - - - +
215B VAL* 4.9 2.2 - - + -
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Residues in contact with ARG 213 (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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9422 G 5.5 7.7 + - - -
9862 G 5.2 7.9 + - - -
9872 A 5.2 4.4 + - - +
103B MET* 4.2 1.1 - - - -
104B ASP* 3.3 2.6 - - - +
105B LEU* 3.1 37.8 + - + +
110B MET* 3.7 38.8 - - + +
122B GLU* 3.9 21.2 + - - -
138B PHE* 3.3 29.8 + - + +
140B VAL* 3.1 45.3 - - + +
211B PHE* 3.6 4.3 + - + -
212B VAL* 1.3 73.7 - - - +
214B LYS* 1.3 79.2 + - - +
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Residues in contact with LYS 214 (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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9432 U 2.1 39.7 + - - +
85B LYS* 5.9 7.0 - - - +
103B MET* 3.3 12.6 - - - +
104B ASP* 4.4 10.3 - - + -
138B PHE* 3.1 45.5 + - + +
212B VAL* 3.3 1.5 - - - +
213B ARG* 1.3 102.3 + - - +
215B VAL* 1.3 77.3 + - - +
216B LYS* 3.9 22.9 - - + +
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Residues in contact with VAL 215 (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 PHE* 3.8 26.7 - - + -
102B GLY* 3.5 6.3 - - - -
103B MET* 2.7 47.6 + - + +
135B LEU* 4.6 5.4 - - + -
136B ARG 3.6 3.1 - - - -
137B LEU* 3.6 27.1 - - + -
188B LEU* 3.9 27.4 - - + -
212B VAL* 4.9 5.4 - - + -
214B LYS* 1.3 82.4 - - - +
216B LYS* 1.3 75.1 + - - +
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Residues in contact with LYS 216 (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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9422 G 2.9 23.3 + - - +
9432 U 2.3 32.6 + - - -
101B HIS 4.4 1.3 - - - -
102B GLY* 5.2 0.2 - - - -
135B LEU* 3.5 15.8 - - - +
136B ARG* 3.0 44.1 + - + +
138B PHE* 4.0 17.3 - - + -
214B LYS* 3.9 28.9 - - - +
215B VAL* 1.3 80.5 - - - +
217B MET* 1.3 64.1 + - - +
218B LEU* 5.0 4.5 - - + -
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Residues in contact with MET 217 (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 PHE* 4.5 11.9 - - + +
101B HIS* 3.0 45.9 + - + +
102B GLY* 5.6 0.2 - - - -
133B TYR* 3.7 25.4 - - + -
134B LEU 3.6 14.8 - - - +
135B LEU* 3.7 17.3 - - + -
181B LEU* 5.6 0.4 - - - -
216B LYS* 1.3 73.3 - - - +
218B LEU* 1.3 69.4 + - - +
219B LYS 3.5 23.8 - - - +
220B LYS* 3.5 37.7 - - + -
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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