Contacts of the strand formed by residues 337 - 342 (chain D) 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 337 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272D GLY* 3.3 7.5 - - - +
319D PHE* 3.5 7.9 - - - +
320D GLY 2.8 33.7 + - - -
327D LEU* 3.5 20.6 - - + -
329D LEU* 3.5 16.4 - - + +
333D ASN* 3.4 24.5 + - - -
335D THR* 3.1 36.2 + - - -
336D ASN* 1.3 74.9 + - - +
338D PHE* 1.3 61.5 + - - +
339D ILE* 3.4 4.6 - - + +
341D THR* 3.3 32.4 + - + +
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Residues in contact with PHE 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D GLY 3.6 20.4 - - - -
270D GLN 3.5 20.2 - - - -
271D PHE 3.9 1.1 - - - -
272D GLY* 3.4 18.2 - - - -
275D GLY* 3.1 13.7 + - - -
276D LEU 3.4 0.5 + - - -
277D GLY 2.9 52.6 + - - +
278D THR* 3.9 24.9 - - + -
280D LEU 4.9 2.2 - - - -
281D PHE* 4.0 23.1 - + - -
336D ASN* 3.8 28.7 - - + -
337D HIS* 1.3 76.6 - - - +
339D ILE* 1.3 63.0 + - + +
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Residues in contact with ILE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D GLY 4.5 2.0 - - - +
276D LEU 5.0 0.2 - - - -
277D GLY* 3.8 19.1 - - - +
278D THR* 6.3 0.7 - - + -
291D ASN* 3.5 28.7 - - - +
319D PHE* 3.5 11.8 - - - +
337D HIS* 4.1 2.9 - - + +
338D PHE* 1.3 88.3 - - + +
340D PRO* 1.4 82.1 - - + +
341D THR* 2.8 22.6 + - - +
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Residues in contact with PRO 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D GLY* 3.4 19.3 - - - +
289D ILE* 3.7 22.7 - - + -
291D ASN* 4.5 9.0 + - + +
292D ILE* 3.8 25.6 - - + +
309D LEU* 4.5 2.7 - - + -
317D TYR* 3.8 20.5 - - + -
319D PHE* 3.5 32.5 - - + -
339D ILE* 1.4 93.4 - - + +
341D THR* 1.3 58.8 + - - +
342D LEU 4.2 0.2 + - - -
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Residues in contact with THR 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D TYR* 3.3 4.0 - - - -
318D THR 2.9 34.3 + - - +
329D LEU* 3.8 24.8 - - + +
337D HIS* 3.3 32.7 + - + +
339D ILE* 2.8 21.0 + - - +
340D PRO* 1.3 72.0 + - - +
342D LEU* 1.3 70.7 + - - +
343D CYS 3.4 0.9 + - - -
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Residues in contact with LEU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D LEU* 4.0 24.9 - - + -
316D MET 3.6 16.6 - - - +
317D TYR* 3.4 38.7 - - + +
329D LEU* 3.6 8.3 - - - +
341D THR* 1.3 77.5 - - - +
343D CYS* 1.3 63.1 + - - +
344D SER* 2.9 15.4 + - - +
347D LEU* 4.0 35.2 - - + -
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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