Contacts of the strand formed by residues 211 - 215 (chain B) in PDB entry 5DVX
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 GLU 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLU 3.7 0.8 - - - +
182B LEU* 3.4 4.7 - - - -
183B SER* 2.9 51.6 + - - +
185B PHE* 3.5 4.9 - - - -
209B GLY* 3.6 10.8 + - - +
210B LEU* 1.3 74.6 - - - +
212B MET* 1.3 61.9 + - - +
213B LYS 4.3 0.2 - - - -
219B GLU* 4.6 11.8 - - - +
220B TYR 3.4 18.1 + - - +
221B ARG* 3.6 21.6 - - - +
257B THR* 4.2 13.2 - - - +
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Residues in contact with MET 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 5.1 3.4 - - - -
181B GLU 3.5 1.8 - - - -
182B LEU* 3.6 27.1 - - + -
185B PHE* 4.8 0.9 - - + -
210B LEU 4.2 0.2 + - - -
211B GLU* 1.3 75.4 - - - +
213B LYS* 1.3 64.6 + - - +
214B LEU* 3.4 39.5 - - + -
219B GLU* 3.6 2.1 - - - -
220B TYR* 2.9 49.7 + - + +
254B HIS* 3.5 46.4 - - + +
273B ALA* 4.2 10.3 - - + -
274B VAL 5.8 0.7 - - - -
275B LEU* 4.5 14.6 - - + +
343B THR* 5.8 0.9 - - - +
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Residues in contact with LYS 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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179B PRO 4.6 1.4 - - - +
180B LEU* 3.9 6.6 - - - -
181B GLU* 2.8 64.0 + - + +
211B GLU 4.3 0.2 - - - -
212B MET* 1.3 76.9 - - - +
214B LEU* 1.3 61.8 + - - +
215B GLY* 3.6 33.4 - - - +
216B PRO* 4.2 9.0 - - - +
218B ARG 3.6 2.0 - - - -
219B GLU* 3.9 30.4 + - + +
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Residues in contact with LEU 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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177B LEU* 5.3 0.2 - - - +
178B ARG* 4.7 9.6 + - - +
179B PRO 5.9 1.3 - - - -
180B LEU* 3.7 22.2 - - + -
212B MET* 3.4 35.0 + - + -
213B LYS* 1.3 72.1 - - - +
215B GLY* 1.3 57.4 + - - +
218B ARG* 2.9 44.4 + - + +
220B TYR* 3.7 23.3 - - + +
273B ALA* 4.4 3.1 - - + -
275B LEU* 5.8 0.2 - - + -
324B TYR* 4.5 10.9 + - - -
326B GLN* 3.9 7.6 - - - +
341B ILE* 3.8 30.3 - - + -
343B THR* 3.7 16.8 - - - +
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Residues in contact with GLY 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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178B ARG* 6.1 4.0 - - - -
213B LYS* 3.4 21.1 - - - +
214B LEU* 1.3 80.9 - - - +
216B PRO* 1.3 79.2 - - - +
217B GLY 3.2 0.5 + - - -
218B ARG* 2.9 24.5 + - - +
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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