Contacts of the strand formed by residues 263 - 268 (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 VAL 263 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256C VAL* 3.8 21.1 - - + -
257C VAL 3.3 10.8 - - - +
258C LEU* 3.8 15.7 - - + -
262C ALA* 1.3 76.0 - - - +
264C TYR* 1.3 63.3 + - - +
288C VAL* 3.4 4.9 - - - +
289C ILE* 2.8 54.0 + - + +
292C ILE* 4.4 12.2 - - + +
297C ILE* 3.7 33.7 - - + -
300C ILE* 4.8 1.3 - - + -
309C LEU* 4.3 10.3 - - + -
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Residues in contact with TYR 264 (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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240C GLU 4.8 6.1 - - - -
241C ILE* 3.8 20.0 - - + -
242C PRO* 3.8 8.6 - - + +
243C GLU* 2.6 39.0 + - - -
256C VAL* 3.4 1.4 - - - +
257C VAL* 2.8 44.5 + - + +
259C THR* 3.8 29.8 - - + -
262C ALA* 4.0 10.7 - - + +
263C VAL* 1.3 79.4 - - - +
265C THR* 1.3 66.6 + - - +
266C PHE* 4.9 0.9 - - + -
286C PRO* 3.8 28.0 - - + -
287C LYS* 3.2 19.5 - - - +
288C VAL* 3.5 23.1 - - + +
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Residues in contact with THR 265 (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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255C THR 3.3 6.5 - - - -
256C VAL* 3.8 26.0 - - + -
264C TYR* 1.3 78.6 - - - +
266C PHE* 1.3 67.3 + - - +
273C GLN 4.6 1.3 - - - +
274C LEU* 2.8 43.8 + - - +
276C LEU* 3.5 18.9 - - - +
283C THR* 3.9 6.4 - - - +
287C LYS* 2.9 28.2 + - - +
289C ILE* 3.8 15.9 - - + +
319C PHE* 4.7 1.3 - - + -
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Residues in contact with PHE 266 (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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211C LEU* 4.3 11.2 - - + -
213C VAL* 4.8 2.9 - - + -
220C GLY 3.7 3.4 - - - +
221C LYS 3.2 28.3 - - - -
222C LEU 3.6 4.9 - - - -
223C GLY* 3.4 26.2 - - - -
238C VAL* 5.2 0.9 - - + -
241C ILE* 4.4 2.2 - - + -
254C HIS* 3.3 2.6 - - - -
255C THR* 2.9 54.6 + - + -
257C VAL* 3.6 26.7 - - + -
264C TYR* 5.0 0.7 - - + -
265C THR* 1.3 83.2 - - - +
267C GLY* 1.3 60.9 + - - +
274C LEU* 3.5 6.6 - - - +
283C THR* 3.7 16.8 - - - +
285C GLU 3.9 13.9 - - - +
286C PRO* 3.6 28.7 - - + -
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Residues in contact with GLY 267 (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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219C ASN 3.1 20.1 - - - +
220C GLY 3.6 1.0 + - - -
221C LYS* 3.7 10.8 - - - -
253C GLU 3.4 9.0 - - - -
266C PHE* 1.3 76.2 - - - +
268C LEU* 1.3 60.5 + - - -
274C LEU* 3.4 6.2 - - - +
282C GLU* 3.4 4.7 - - - -
283C THR 2.8 33.8 + - - -
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Residues in contact with LEU 268 (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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219C ASN* 3.4 42.7 + - + +
253C GLU* 2.8 28.4 + - + +
254C HIS* 3.8 7.1 - - - +
267C GLY* 1.3 72.3 - - - -
269C GLY* 1.3 68.5 + - - +
270C GLN* 3.5 45.2 - - + +
273C GLN* 3.5 15.2 + - - -
274C LEU* 4.3 2.0 - - - -
281C PHE* 3.8 11.2 - - + +
282C GLU* 4.3 14.8 - - + +
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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