Contacts of the strand formed by residues 317 - 321 (chain B) in PDB entry 1HJX
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 PRO 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B HIS* 3.1 24.1 + - - -
308B VAL* 4.1 5.6 - - + -
309B HIS 3.3 11.2 - - - +
310B ARG* 3.8 29.4 - - - +
316B VAL* 1.3 87.1 - - + +
318B TYR* 1.3 61.5 + - - +
328B TYR* 3.2 54.7 + - + +
330B ASP* 3.9 14.8 - - - +
333B SER* 3.8 8.7 - - - +
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 3.3 27.9 + - - -
273B GLY* 3.5 12.1 - - - -
274B VAL* 4.2 11.9 - - + -
308B VAL* 3.4 3.8 - - - +
309B HIS* 2.9 78.4 + + + +
311B ILE* 3.6 29.4 - - + -
317B PRO* 1.3 75.6 - - - +
319B ALA* 1.3 65.0 + - - +
320B THR* 4.6 3.4 - - + -
325B TRP* 3.3 40.8 - + + -
326B VAL 3.1 14.4 - - - +
327B GLY* 4.2 1.6 - - - -
328B TYR* 3.8 3.8 - - - -
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Residues in contact with ALA 319 (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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302B PHE* 3.9 14.2 - - + -
303B LEU* 3.4 33.4 - - + -
306B ALA* 4.3 2.0 - - + -
307B THR 3.2 11.0 - - - +
308B VAL* 4.2 2.2 - - + -
318B TYR* 1.3 77.6 - - - +
320B THR* 1.3 62.2 + - - +
325B TRP* 3.5 2.8 - - - -
326B VAL* 2.8 34.7 + - + +
328B TYR* 3.7 9.8 - - + -
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Residues in contact with THR 320 (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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267B LEU* 3.6 19.6 - - - +
272B THR* 4.0 21.6 - - + +
302B PHE* 4.2 1.3 - - - -
306B ALA* 3.6 1.7 - - - -
307B THR* 3.0 41.0 + - - +
309B HIS* 4.3 18.6 - - + +
318B TYR* 4.6 1.3 - - + -
319B ALA* 1.3 77.1 - - - +
321B LYS* 1.3 61.5 + - - +
322B GLY 4.3 1.4 + - - -
324B GLN 2.9 18.6 + - - -
325B TRP* 4.0 14.2 - - - -
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Residues in contact with LYS 321 (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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301B ASP 4.2 2.6 + - - -
302B PHE* 2.9 48.3 + - + +
304B ARG 2.9 14.2 + - - +
305B GLY* 3.4 33.0 - - - +
306B ALA* 3.6 8.3 - - + +
320B THR* 1.3 78.1 + - - +
322B GLY* 1.3 69.3 + - - +
323B ASN 3.3 0.2 + - - -
324B GLN* 3.0 24.9 + - - +
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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