Contacts of the strand formed by residues 261 - 267 (chain F) in PDB entry 2HU4
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 261 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F THR* 2.6 35.0 + - - +
213F ASP* 3.9 12.6 - - - +
257F MET* 3.1 4.0 - - - -
258F GLU 2.8 35.7 + - - +
259F LYS* 4.6 2.5 - - + +
260F GLY* 1.3 79.6 - - - +
262F VAL* 1.3 76.4 + - - +
263F VAL* 3.3 10.6 + - + +
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Residues in contact with VAL 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F LEU* 4.0 12.8 - - + -
213F ASP* 2.9 22.3 + - - +
215F ILE* 3.9 29.6 - - + -
255F PHE* 4.0 16.8 - - + -
256F LYS 3.6 6.5 - - - +
257F MET* 4.0 6.7 - - - -
261F LYS* 1.3 79.3 - - - +
263F VAL* 1.3 61.5 + - - +
264F LYS* 3.8 23.8 - - - +
265F SER* 4.5 4.3 - - - +
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Residues in contact with VAL 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F LYS* 2.9 47.0 + - + +
257F MET 4.4 0.4 - - - +
258F GLU* 4.3 27.6 - - + +
261F LYS* 3.5 19.7 - - + +
262F VAL* 1.3 75.7 - - - +
264F LYS* 1.3 65.7 + - + +
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Residues in contact with LYS 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F PHE* 3.8 0.5 - - - -
256F LYS* 2.9 39.2 + - + +
262F VAL* 3.6 6.2 - - - +
263F VAL* 1.3 89.0 - - + +
265F SER* 1.3 70.9 + - - +
266F VAL* 4.4 14.1 - - - -
309F ASN* 3.3 39.7 + - - +
310F LEU* 3.6 12.3 - - + +
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Residues in contact with SER 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F LYS* 5.2 10.7 + - - -
254F ILE 3.4 6.3 - - - -
255F PHE* 3.7 33.2 - - - -
262F VAL* 4.5 4.8 - - - +
264F LYS* 1.3 81.6 - - - +
266F VAL* 1.3 66.7 + - - +
267F GLU 4.4 0.2 + - - -
310F LEU* 3.8 1.1 - - - -
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Residues in contact with VAL 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F LYS* 3.4 5.7 - - - -
254F ILE* 3.0 36.0 + - + +
264F LYS* 4.4 13.5 - - - -
265F SER* 1.3 79.2 - - - +
267F GLU* 1.3 67.9 + - - +
268F LEU* 3.7 2.6 + - + +
309F ASN 5.0 0.2 - - - +
310F LEU* 3.6 34.7 - - + +
312F TYR* 3.7 33.4 - - + -
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Residues in contact with GLU 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F TRP* 4.4 4.4 + - - -
219F ARG* 4.6 11.8 + - - -
251F SER* 2.8 29.3 + - - +
252F TYR 3.5 9.2 - - - +
253F LYS* 3.7 26.6 + - - +
265F SER 4.4 0.6 + - - -
266F VAL* 1.3 79.0 - - - +
268F LEU* 1.3 74.1 + - - +
269F ASP* 3.3 5.2 + - - +
312F TYR* 4.2 2.6 + - - -
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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