Contacts of the strand formed by residues 254 - 259 (chain C) in PDB entry 4JHN
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 HIS 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C HIS* 3.5 5.1 - - - -
221C LYS* 4.4 0.7 - - - -
251C GLY* 2.8 36.3 + - - -
252C GLY 3.7 0.2 - - - -
253C GLU* 1.3 82.3 + - - +
255C THR* 1.3 67.2 + - - +
256C VAL* 3.8 16.2 - - + -
266C PHE 3.3 11.7 - - - +
267C GLY* 4.3 0.4 - - - -
268C LEU 3.8 11.9 - - - +
273C GLN* 3.4 38.6 + - + +
274C LEU* 3.9 10.1 - - + -
302C CYS* 3.6 9.4 - - + -
303C GLY 3.6 24.0 - - - -
304C GLU 4.0 10.8 + - - -
306C HIS 3.8 7.2 + - - -
307C THR* 3.0 20.2 + - - -
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C HIS* 2.8 16.4 + - + -
203C ALA* 5.3 2.5 - - + -
213C VAL* 5.4 2.2 - - + -
221C LYS 2.7 22.1 + - - -
248C VAL* 3.7 25.6 - - + -
249C ALA 3.5 6.5 - - - +
250C CYS* 4.1 9.4 - - - -
254C HIS* 1.3 72.2 - - - +
256C VAL* 1.3 69.7 + - - +
257C VAL* 4.3 0.4 - - + -
265C THR* 3.3 6.9 - - - -
266C PHE* 2.9 63.0 + - + -
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C VAL* 3.4 5.0 - - - +
249C ALA 2.8 32.5 + - - -
254C HIS* 3.8 11.7 - - + -
255C THR* 1.3 76.8 - - - +
257C VAL* 1.3 65.5 + - - +
263C VAL* 3.8 24.5 - - + -
264C TYR 3.4 3.4 - - - +
265C THR* 3.8 11.0 - - + -
300C ILE* 3.3 25.0 - - + +
302C CYS* 3.2 30.3 - - - -
307C THR* 3.7 21.1 - - + +
309C LEU* 4.5 0.9 - - + -
319C PHE* 5.6 0.2 - - + -
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LEU* 3.7 16.8 - - + -
241C ILE* 4.1 9.6 - - + -
245C VAL* 3.6 38.4 - - + -
247C GLN 3.5 3.8 - - - +
248C VAL* 4.1 8.5 - - + -
255C THR* 4.3 0.2 - - + -
256C VAL* 1.3 79.8 - - - +
258C LEU* 1.3 65.1 + - - +
259C THR* 4.3 3.8 - - + -
262C ALA 4.0 0.3 - - - +
263C VAL* 3.3 7.9 - - - +
264C TYR* 2.8 47.9 + - + +
266C PHE* 3.6 32.1 - - + -
300C ILE* 4.0 2.7 - - - -
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C VAL* 3.8 2.4 - - - +
246C ILE* 2.8 40.8 + - + -
247C GLN* 2.9 56.9 + - + +
257C VAL* 1.3 72.8 - - - +
259C THR* 1.3 71.1 + - - +
262C ALA 3.9 2.2 - - - +
263C VAL* 3.8 14.1 - - + -
297C ILE* 3.5 46.4 - - + +
298C SER* 3.9 9.9 - - - +
299C TYR 4.2 1.6 - - - +
300C ILE* 3.8 10.6 - - + +
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Residues in contact with THR 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ILE* 3.8 17.7 - - + -
243C GLU* 3.8 11.7 + - - +
244C LYS 3.4 18.6 - - - +
245C VAL* 4.1 9.6 - - + -
246C ILE* 3.9 9.8 - - - +
257C VAL* 4.3 2.2 - - + -
258C LEU* 1.3 91.3 - - - +
260C GLU* 1.3 65.7 + - - +
261C ASN* 3.3 3.2 + - - -
262C ALA* 2.9 36.0 + - - +
264C TYR* 3.8 29.0 - - + -
297C ILE 5.4 0.2 - - - +
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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