Contacts of the strand formed by residues 322 - 329 (chain B) in PDB entry 3HI7
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 TRP 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A PRO* 5.7 1.6 - - - +
293A SER* 5.2 0.5 - - - -
317B VAL 4.5 0.2 - - - -
318B LEU* 3.4 6.6 - - - +
319B TYR* 2.8 66.3 + + + +
320B GLY 4.2 1.7 - - - +
321B GLY* 1.3 78.8 - - - +
323B SER* 1.3 62.2 + - - +
324B PHE* 4.5 11.4 - + + -
339B VAL* 3.6 25.6 - - + -
340B HIS 3.4 20.2 - - - -
341B PHE* 3.4 14.6 - + - -
346B ILE* 4.0 15.7 - - + -
469B PHE* 3.7 29.3 - + + +
470B TYR 2.8 20.3 + - - -
471B PRO* 5.1 1.8 - - + -
473B GLY* 3.4 30.1 - - - -
474B VAL 3.4 21.1 - - - -
475B MET* 3.8 19.3 - - + -
593B TYR* 5.5 0.4 - + - -
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PRO* 6.6 0.4 - - - -
317B VAL 3.3 7.0 + - - -
318B LEU* 3.5 20.2 - - - +
321B GLY 3.9 0.6 + - - -
322B TRP* 1.3 73.9 - - - +
324B PHE* 1.3 66.3 + - - +
338B ASN 3.4 3.8 + - - +
339B VAL* 4.5 0.2 - - - +
340B HIS* 2.8 46.3 + - - +
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 5.6 0.4 - - - -
316B ALA* 3.5 3.6 - - - +
317B VAL* 2.8 73.1 + - + +
322B TRP* 4.5 13.0 - + + -
323B SER* 1.3 80.1 + - - +
325B ALA* 1.3 72.9 + - - +
326B PHE* 4.5 1.6 - + - -
336B VAL* 4.1 14.4 - - + -
337B LEU 3.8 11.7 - - - +
338B ASN 3.9 3.8 - - - -
339B VAL* 3.9 16.6 - - + -
418B LEU* 4.9 4.0 - - + -
450B LEU* 4.0 10.1 - - + -
452B LEU* 4.4 11.2 - - + -
469B PHE* 3.5 50.3 - + - -
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Residues in contact with ALA 325 (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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30B ALA* 3.7 22.7 - - + -
33B PHE* 3.7 27.1 - - + -
315B ASN* 3.1 16.6 - - - +
316B ALA* 4.5 0.2 - - - +
324B PHE* 1.3 81.1 - - - +
326B PHE* 1.3 62.5 + - - +
336B VAL* 3.4 4.7 - - - -
337B LEU* 2.8 34.1 + - + +
338B ASN* 5.1 1.8 - - + +
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Residues in contact with PHE 326 (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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34B SER* 4.8 0.7 - - - -
35B ASP 5.4 0.2 + - - -
312B LEU* 3.8 5.6 - - + -
314B GLY 4.1 5.8 - - - -
315B ASN* 3.0 65.0 + - + +
317B VAL* 3.8 26.7 - - + -
324B PHE* 4.5 1.3 - + + -
325B ALA* 1.3 76.4 - - - +
327B ARG* 1.3 67.7 + - - +
328B LEU 5.3 0.4 - - - -
334B LEU* 5.2 0.2 - - + -
335B GLN 3.3 14.4 - - - +
336B VAL* 4.3 2.0 - - + +
337B LEU* 4.5 4.5 - - - -
398B LEU* 3.8 25.4 - - + -
416B LEU* 4.2 29.6 - - + -
418B LEU* 5.2 0.4 - - + -
452B LEU* 3.6 29.4 - - + -
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Residues in contact with ARG 327 (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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33B PHE* 3.3 21.3 - - - +
35B ASP* 2.9 33.1 + - - +
73B GLU* 4.5 4.0 - - - +
74B MET* 3.2 60.4 + - - +
76B LEU* 4.6 13.7 - - - +
326B PHE* 1.3 83.0 - - - +
328B LEU* 1.3 59.0 + - - +
329B ARG* 4.0 36.7 - - - +
334B LEU* 3.7 7.3 - - - +
335B GLN* 2.8 63.5 + - + +
337B LEU* 3.9 9.4 - - + +
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Residues in contact with LEU 328 (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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35B ASP* 2.8 27.7 + - - +
327B ARG* 1.3 72.0 - - - +
329B ARG* 1.3 64.1 + - - +
330B SER* 3.3 7.4 + - - -
333B GLY* 3.8 23.3 - - - -
334B LEU* 3.9 7.6 - - + +
379B GLY 3.8 18.4 - - - +
382B THR* 3.7 32.5 - - + +
400B THR* 4.3 13.9 - - + +
402B HIS* 4.1 6.1 - - + -
415B ALA* 4.6 0.2 - - + -
416B LEU* 3.8 39.5 - - + -
454B THR* 4.0 11.7 - - + +
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Residues in contact with ARG 329 (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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35B ASP* 4.1 0.2 + - - -
73B GLU* 3.4 14.7 + - - +
74B MET 5.2 1.6 + - - -
75B LEU* 6.2 2.6 - - - +
98B ARG* 3.6 23.4 - - - +
327B ARG* 3.9 32.1 - - - +
328B LEU* 1.3 70.8 - - - +
330B SER* 1.3 62.9 + - - +
331B SER* 3.1 22.7 + - - +
332B SER* 2.9 35.7 + - - +
333B GLY 2.8 42.3 + - - +
335B GLN* 3.6 20.5 - - - +
353B GLN* 5.6 1.8 + - - +
374B VAL* 6.2 0.2 - - - +
379B GLY* 3.3 5.0 - - - -
633B CYS* 3.7 30.9 - - - -
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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