Contacts of the strand formed by residues 257 - 263 (chain N) in PDB entry 5X22
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 GLY 257 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255N GLU 4.1 1.2 + - - -
256N GLU* 1.3 74.7 - - - +
258N VAL* 1.3 64.7 + - - -
259N VAL 3.9 0.2 + - - -
272N LEU* 4.7 6.4 - - - +
273N ARG 3.7 16.6 - - - -
274N ARG* 4.3 5.2 - - - -
297N ILE* 4.0 7.8 - - - +
298N VAL* 3.4 34.6 + - - +
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Residues in contact with VAL 258 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N GLY* 1.3 71.9 - - - -
259N VAL* 1.3 64.3 + - - +
271N VAL 3.5 3.8 - - - +
272N LEU* 3.6 1.0 - - - -
273N ARG* 2.9 58.1 + - + +
275N GLU 4.8 6.7 - - - +
295N GLY* 3.4 32.1 - - - +
296N GLU 3.8 2.5 - - - -
297N ILE* 3.7 18.3 - - + +
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Residues in contact with VAL 259 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258N VAL* 1.3 74.5 - - - +
260N GLU* 1.3 68.6 + - - +
261N LEU* 4.0 4.5 - - + +
270N LEU* 3.6 22.0 - - + -
271N VAL 3.6 2.5 - - - -
272N LEU* 3.8 23.3 - - + -
273N ARG* 5.6 0.4 - - - -
292N VAL* 4.2 11.7 - - + -
293N VAL 3.5 22.2 - - - +
294N HIS* 3.7 2.6 + - - -
295N GLY* 2.7 31.9 + - - -
296N GLU 3.0 21.7 + - - +
298N VAL* 3.8 23.1 - - + -
304N LEU* 5.0 0.4 - - + -
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Residues in contact with GLU 260 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258N VAL 3.8 0.6 + - - -
259N VAL* 1.3 73.4 - - - +
261N LEU* 1.3 65.5 + - - +
262N LYS* 3.7 17.9 + - + +
269N PHE 3.9 0.2 - - - +
270N LEU* 3.7 1.0 - - - -
271N VAL* 2.9 54.8 + - + +
273N ARG* 2.4 44.0 + - - +
294N HIS* 3.5 23.8 - - + +
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Residues in contact with LEU 261 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259N VAL* 3.9 7.7 - - + -
260N GLU* 1.3 72.8 - - - +
262N LYS* 1.3 58.6 + - - +
263N GLU* 3.6 31.2 + - + +
268N ALA* 4.3 16.8 - - + -
269N PHE 3.4 18.2 - - - +
270N LEU* 4.2 19.3 - - + -
284N LEU* 4.9 0.2 - - + -
290N PRO* 4.6 14.8 - - + -
292N VAL 3.6 22.9 - - - +
293N VAL* 4.6 5.8 - - - -
294N HIS* 3.3 34.7 - - + +
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Residues in contact with LYS 262 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217N LYS* 4.1 17.8 - - - +
219N GLU* 6.3 0.4 - - - +
260N GLU* 3.7 19.6 + - + +
261N LEU* 1.3 71.8 - - - +
263N GLU* 1.3 66.2 + - - +
264N LEU* 3.7 6.2 + - + +
269N PHE* 2.9 54.9 + - + +
271N VAL* 6.0 2.9 - - + -
339N TRP* 4.5 7.6 - - + -
341N GLU* 3.2 35.7 + - - +
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Residues in contact with GLU 263 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261N LEU* 3.6 35.4 + - + +
262N LYS* 1.3 77.3 - - - +
264N LEU* 1.3 69.6 + - - +
267N GLY 4.4 4.0 - - - +
268N ALA* 4.6 7.0 - - + +
290N PRO* 5.2 6.1 - - - +
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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