Contacts of the strand formed by residues 349 - 356 (chain B) 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 PHE 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 4.5 16.4 - - + -
15B PHE* 4.1 22.9 - + - -
313B ILE 5.2 0.3 - - - +
314B GLY 3.8 9.5 - - - +
315B LEU* 5.5 2.9 - - - +
345B ASN 4.4 7.2 - - - -
346B PHE* 2.8 47.3 + + + +
347B LEU 3.2 4.4 - - - +
348B ARG* 1.3 92.7 - - + +
350B ILE* 1.3 68.3 + - - +
351B VAL 3.9 0.2 - - - -
365B ALA* 4.1 19.3 - - + -
366B ALA 3.3 7.2 - - - +
367B PRO* 3.5 37.9 - - + -
368B HIS* 3.9 2.4 - - - +
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Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ARG* 3.4 19.5 - - - +
313B ILE 3.4 22.9 - - - +
314B GLY* 3.9 9.4 - - - -
349B PHE* 1.3 76.3 - - - +
351B VAL* 1.3 71.9 + - - +
352B LYS* 3.4 24.9 + - + +
365B ALA* 3.3 1.8 - - - -
366B ALA* 2.7 40.2 + - + +
367B PRO 5.2 0.9 - - - +
368B HIS* 3.7 24.0 - - + +
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ILE* 3.4 46.4 - - + +
314B GLY* 2.9 26.5 + - - +
316B MET* 3.9 28.0 - - + +
346B PHE* 4.1 30.5 - - + -
349B PHE 5.3 0.2 - - - +
350B ILE* 1.3 73.7 - - - +
352B LYS* 1.3 60.9 + - - +
353B LEU 4.1 2.9 - - - +
363B VAL* 3.7 23.1 - - + -
364B PHE 3.9 3.1 - - - -
365B ALA* 4.1 7.2 - - + -
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SER 5.0 0.2 - - - +
310B ILE* 4.1 9.4 - - - +
350B ILE* 3.5 29.9 - - + +
351B VAL* 1.3 75.2 - - - +
353B LEU* 1.3 73.6 + - + +
364B PHE* 2.8 41.2 + - + +
366B ALA* 4.0 21.9 - - + +
190D LYS* 5.2 2.8 - - - +
210D GLU* 3.3 27.9 + - - -
212D TYR* 4.8 3.6 + - - -
237D LEU* 3.9 21.4 - - + +
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PRO* 4.0 6.7 - - + +
38B VAL* 3.6 37.0 - - - +
39B HIS* 3.8 12.6 - - + +
40B LEU* 3.7 22.4 - - + +
299B TYR* 6.0 0.7 - - - -
310B ILE* 4.2 4.7 - - - -
351B VAL* 4.1 0.5 - - - +
352B LYS* 1.3 85.2 - - + +
354B VAL* 1.3 62.3 + - - +
363B VAL* 3.3 6.4 - - - +
364B PHE* 2.8 55.2 + - + +
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.3 5.0 - - - +
299B TYR* 3.6 26.7 + - + -
301B SER* 3.8 20.6 + - - -
308B ALA* 4.1 12.6 - - + +
310B ILE* 3.6 26.8 - - + +
316B MET* 3.8 25.1 - - - -
353B LEU* 1.3 76.2 - - - +
355B ALA* 1.3 68.0 + - - +
361B MET* 4.0 22.0 - - + -
362B VAL 3.4 11.2 - - - +
363B VAL* 4.3 3.8 - - + -
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 3.9 15.5 - - + +
41B SER* 3.8 12.6 - - - -
42B CYS* 3.5 33.7 - - - +
301B SER* 3.8 4.7 - - - -
354B VAL* 1.3 75.6 - - - +
356B CYS* 1.3 63.9 + - - +
361B MET* 3.4 4.5 - - - +
362B VAL 2.9 33.4 + - - +
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Residues in contact with CYS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B CYS* 3.6 14.2 - - - +
301B SER* 3.5 19.2 + - - -
302B CYS 3.3 16.3 + - - +
303B GLY* 3.4 22.9 - - - +
306B HIS* 3.4 26.9 - - - +
308B ALA* 3.7 30.5 - - - -
354B VAL* 4.5 0.7 - - - -
355B ALA* 1.3 77.3 - - - +
357B GLY* 1.3 59.2 + - - +
360B HIS 3.9 3.6 - - - -
361B MET* 3.9 6.7 - - - -
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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