Contacts of the helix formed by residues 328 - 342 (chain B) in PDB entry 3V9H
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 ASP 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A PRO* 4.5 13.4 - - + +
326B SER 3.7 0.2 + - - -
327B ALA* 1.3 68.0 - - - +
329B VAL* 1.3 65.6 + - - +
330B GLU* 3.6 10.4 + - - +
331B SER* 2.8 46.7 + - - +
332B VAL* 3.0 21.5 + - - +
483B PHE* 5.1 1.4 - - - +
485B GLN* 3.5 29.3 + - - +
507B ASN* 5.6 1.8 + - - -
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA 3.1 8.1 + - - +
328B ASP* 1.3 73.2 + - - +
330B GLU* 1.3 70.8 + - + +
332B VAL* 3.3 8.5 + - - +
333B VAL* 2.9 29.1 + - + +
360B LEU* 3.9 34.3 - - + -
363B GLN* 3.8 38.8 - - + +
364B ILE* 4.0 22.4 - - + +
367B ARG* 4.4 9.6 - - + -
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A GLY 6.2 0.2 - - - -
328B ASP* 3.2 11.5 + - - +
329B VAL* 1.3 82.7 - - + +
331B SER* 1.3 59.0 + - - +
333B VAL* 3.2 8.1 + - - +
334B SER* 3.0 32.6 + - - -
363B GLN* 5.7 0.5 + - - -
367B ARG* 2.6 50.5 + - - +
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PRO* 3.5 7.6 - - - +
554A LEU* 2.9 42.7 + - - +
555A GLY 5.7 0.2 - - - +
328B ASP* 2.8 34.8 + - - +
330B GLU* 1.3 71.0 - - - +
332B VAL* 1.3 66.9 + - - +
334B SER* 3.6 5.8 + - - -
335B GLY* 2.9 23.6 + - - -
483B PHE* 3.8 13.5 - - - -
507B ASN* 5.8 3.4 - - - -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 3.8 26.0 - - + -
327B ALA* 3.8 13.0 - - + -
328B ASP 3.0 15.7 + - - +
329B VAL* 3.4 10.8 - - - +
331B SER* 1.3 76.6 - - - +
333B VAL* 1.3 57.8 + - - +
336B THR* 2.5 44.7 + - - +
354B LEU* 4.5 5.6 - - + -
364B ILE* 4.1 22.0 - - + -
368B LEU* 6.4 0.4 - - + -
483B PHE* 3.6 37.9 - - + -
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A TRP* 5.4 0.7 - - + -
329B VAL* 2.9 25.7 + - + +
330B GLU* 3.2 11.0 + - - +
332B VAL* 1.3 77.6 - - - +
334B SER* 1.3 59.7 + - - +
336B THR* 3.9 0.9 - - - -
337B LEU* 2.9 53.4 + - + +
364B ILE* 4.3 16.8 - - + +
367B ARG* 3.6 39.3 - - + +
368B LEU* 4.1 16.9 - - + +
371B GLU* 4.2 9.0 - - + -
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LEU* 3.8 11.8 - - - +
555A GLY 3.0 28.9 + - - -
556A ASP* 4.7 0.2 - - - -
557A TRP* 3.8 26.6 - - - +
330B GLU* 3.0 16.4 + - - -
331B SER* 3.6 3.3 + - - -
333B VAL* 1.3 79.4 - - - +
335B GLY* 1.3 60.6 + - - +
337B LEU* 3.3 2.1 + - - +
338B ARG* 2.9 36.0 + - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LEU* 4.1 12.1 - - - +
321B HIS* 3.8 7.9 - - - -
331B SER 2.9 17.4 + - - -
334B SER* 1.3 80.4 + - - +
336B THR* 1.3 56.4 + - - +
338B ARG* 3.7 3.7 - - - +
339B SER* 2.8 24.9 + - - -
483B PHE* 4.8 1.6 - - - -
509B LYS* 3.4 25.2 - - - +
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Residues in contact with THR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B HIS* 3.0 26.6 + - - +
332B VAL* 2.5 35.1 + - - +
333B VAL* 4.0 3.1 - - - -
335B GLY* 1.3 72.2 - - - +
337B LEU* 1.3 61.1 + - - +
340B ALA* 2.8 35.6 + - - +
351B CYS* 4.2 14.1 - - - -
354B LEU* 4.1 16.6 - - + +
368B LEU* 5.0 6.1 - - + -
453B LEU* 3.8 28.5 - - + -
483B PHE* 5.2 0.2 - - - -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A TRP* 3.8 24.0 - - + +
333B VAL* 2.9 33.0 + - + +
334B SER 3.7 3.6 - - - +
336B THR* 1.3 75.8 - - - +
338B ARG* 1.3 63.4 + - - +
341B PHE* 3.1 56.7 + - + +
368B LEU* 3.8 26.0 - - + +
371B GLU* 3.5 32.5 - - + -
372B HIS* 4.8 1.6 - - - +
375B ILE* 4.4 10.8 - - + -
387B PHE* 4.0 8.4 - - + -
433B ILE* 4.9 3.6 - - + -
453B LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LEU 5.9 1.6 + - - -
556A ASP 3.2 12.8 + - - -
557A TRP* 2.7 29.5 + - + +
558A SER 3.0 26.7 + - - -
559A TYR* 3.3 40.4 + - - -
334B SER* 2.9 21.0 + - - +
335B GLY* 3.7 3.8 - - - +
337B LEU* 1.3 77.0 - - - +
339B SER* 1.3 63.6 + - - +
342B GLU* 3.0 50.9 + - - +
387B PHE* 4.1 3.1 - - + -
509B LYS* 3.8 23.6 - - + +
511B THR* 4.9 0.3 + - - +
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B HIS* 3.7 19.1 - - - -
335B GLY 2.8 21.0 + - - -
336B THR 4.2 0.2 - - - -
338B ARG* 1.3 74.7 - - - +
340B ALA* 1.3 63.0 + - - +
342B GLU* 4.6 2.6 + - - +
345B GLY* 4.8 0.9 - - - -
347B LYS* 5.5 0.9 - - - +
350B ALA* 3.4 19.4 - - - +
351B CYS* 2.7 31.2 + - - +
509B LYS* 4.0 9.1 - - - +
510B SER* 2.9 14.0 + - - -
511B THR* 3.6 20.1 - - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B THR 2.8 23.4 + - - +
339B SER* 1.3 77.1 - - - +
341B PHE* 1.3 72.4 + - + +
345B GLY* 3.3 19.6 - - - -
350B ALA* 4.7 0.9 - - - +
351B CYS* 3.3 24.9 - - + +
450B GLY 4.3 1.7 - - - +
451B PRO* 3.9 4.5 - - - +
452B VAL 4.6 0.7 + - - -
453B LEU* 4.0 29.4 - - + -
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Residues in contact with PHE 341 (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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337B LEU* 3.1 46.9 + - + +
340B ALA* 1.3 91.8 - - + +
342B GLU* 1.3 64.6 + - - +
344B GLY* 2.7 22.3 + - - -
345B GLY 3.7 2.5 - - - +
372B HIS* 4.8 2.2 - + - -
375B ILE* 4.3 6.3 - - + -
387B PHE* 4.2 6.3 - - + -
388B PHE* 3.2 28.6 - - + -
431B PRO* 3.9 18.8 - - + -
432B CYS 3.5 20.9 - - - -
433B ILE* 3.9 19.3 - - + -
451B PRO* 3.2 38.8 - - + -
452B VAL 4.1 0.9 - - - -
453B LEU* 4.0 15.3 - - + -
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A TYR* 2.3 44.0 + - - -
157B GLN* 3.3 25.1 + - + +
337B LEU 4.0 0.4 + - - -
338B ARG* 3.0 39.9 + - - +
339B SER 4.6 2.2 + - - +
341B PHE* 1.3 75.8 - - - +
343B TYR* 1.3 69.5 - - - +
345B GLY* 2.9 14.7 + - - -
346B GLN 4.1 0.7 + - - -
347B LYS* 4.3 18.2 + - - +
387B PHE* 3.7 24.4 - - + +
388B PHE* 4.6 3.1 - - - -
509B LYS* 4.0 11.8 + - - -
511B THR* 4.4 2.4 + - + +
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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
------------------------------------------------------------
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