Contacts of the strand formed by residues 297 - 302 (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 ILE 297 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C LEU* 3.5 36.8 - - + +
259C THR 5.4 0.2 - - - +
263C VAL* 3.7 18.2 - - + -
292C ILE* 4.1 21.8 - - + -
295C GLN* 3.8 8.2 + - + +
296C THR* 1.3 81.0 - - - +
298C SER* 1.3 61.7 + - - +
299C TYR 3.5 18.8 - - - +
300C ILE* 3.9 11.0 - - + -
309C LEU* 4.0 22.0 - - + -
310C ILE 3.5 8.7 - - - +
311C THR* 3.8 26.9 - - + -
317C TYR* 5.0 2.9 - - + -
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Residues in contact with SER 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C GLN* 3.0 17.8 - - - +
258C LEU* 3.9 5.8 - - - +
296C THR* 3.8 1.9 + - - -
297C ILE* 1.3 73.7 - - - +
299C TYR* 1.3 65.1 + - - +
310C ILE* 2.8 20.4 + - - +
311C THR 3.3 11.8 + - - -
312C ASP* 4.2 18.1 - - - -
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Residues in contact with TYR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C HIS* 6.0 1.7 - - - -
40C LEU 5.6 1.9 + - - -
194C TRP* 4.0 23.5 - + - -
247C GLN* 3.5 17.5 - - - +
297C ILE* 3.5 7.8 - - - +
298C SER* 1.3 84.6 + - - +
300C ILE* 1.3 84.9 + - - +
301C SER* 3.9 6.8 + - - -
309C LEU* 3.5 1.2 - - - -
310C ILE* 2.9 45.7 + - + -
353C LEU* 6.0 0.4 - - - -
354C VAL* 3.6 39.6 + - + -
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Residues in contact with ILE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C TRP* 5.5 1.3 - - - +
247C GLN* 3.1 19.7 + - + +
248C VAL* 3.9 6.7 - - - +
249C ALA* 3.7 19.0 - - + +
256C VAL* 3.3 46.9 - - + +
258C LEU* 3.8 28.5 - - + +
263C VAL* 4.8 2.7 - - + -
297C ILE* 3.9 11.2 - - + -
299C TYR* 1.3 98.8 + - - +
301C SER* 1.3 61.0 + - - +
308C ALA 3.6 3.4 - - - -
309C LEU* 3.6 22.0 - - + -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ALA* 4.3 3.6 - - - -
299C TYR* 3.9 7.5 + - - -
300C ILE* 1.3 75.9 - - - +
302C CYS* 1.3 66.6 + - - +
307C THR* 3.4 8.3 - - - +
308C ALA 2.8 31.4 + - - +
354C VAL* 3.9 25.8 - - - -
355C ALA* 3.8 5.7 - - - -
356C CYS* 3.4 29.6 + - - -
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Residues in contact with CYS 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ALA* 3.4 31.7 - - + +
250C CYS 4.2 7.6 - - - +
251C GLY* 4.2 11.4 - - - -
254C HIS* 3.6 13.9 - - - +
256C VAL* 3.2 35.4 - - - -
301C SER* 1.3 79.9 + - - +
303C GLY* 1.3 66.0 + - - +
306C HIS 3.4 6.3 - - - +
307C THR* 4.2 0.9 - - - -
356C CYS* 3.3 17.3 - - - +
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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
------------------------------------------------------------
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