Contacts of the helix formed by residues 377 - 392 (chain B) in PDB entry 3VF1
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 CYS 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B THR 3.7 16.4 - - - -
373B HIS 3.1 12.4 + - - +
375B LEU 4.1 0.4 - - - -
376B ARG* 1.3 83.6 - - - +
378B HIS* 1.3 67.9 + - - +
379B LEU 3.6 0.2 - - - -
381B MET* 3.1 29.1 + - - +
551B THR* 4.2 7.9 - - - -
555B GLN* 3.8 28.0 - - - -
556B HIS* 3.9 28.5 - - + -
559B VAL* 4.2 6.1 - - - -
677B ILE* 3.4 15.7 - - + +
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Residues in contact with HIS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS* 3.1 27.4 + + - -
374B LEU* 3.0 25.2 + - + +
377B CYS* 1.3 82.9 - - - +
379B LEU* 1.3 66.2 + - + +
382B GLU 3.4 11.6 + - - -
409B ILE* 3.5 5.7 - - - +
412B ILE* 4.0 13.3 - - + +
413B ASN* 2.9 38.6 + - - +
420B LEU* 5.9 3.3 - - + +
556B HIS* 3.3 10.4 + + - -
677B ILE* 3.5 17.8 - - + +
679B ILE* 3.1 19.2 + - - -
701B FE2 2.2 31.9 - - - -
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 6.2 1.1 - - + -
158B LEU* 4.6 13.2 - - + -
159B PRO* 3.4 23.2 - - + +
160B GLY 4.4 1.0 - - - +
374B LEU* 2.9 17.5 + - + +
375B LEU* 3.7 15.5 - - + +
378B HIS* 1.3 74.4 - - + +
380B MET* 1.3 64.5 + - - +
382B GLU* 3.5 4.3 + - - +
383B PRO* 3.1 18.9 - - - +
413B ASN* 3.8 20.2 - - + +
417B ARG* 4.2 18.6 - - + +
421B ILE* 4.3 19.1 - - + -
442B MET* 3.9 34.5 - - + -
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PRO* 3.7 22.2 - - + -
375B LEU* 2.9 26.2 + - + +
376B ARG* 3.9 7.9 - - + +
377B CYS 4.0 0.2 + - - -
378B HIS 3.5 0.2 - - - -
379B LEU* 1.3 76.3 - - - +
381B MET* 1.3 62.5 + - + +
382B GLU 3.5 0.2 - - - -
383B PRO* 3.5 0.6 - - - +
446B TYR* 3.8 17.9 - - + -
449B VAL* 4.5 17.3 - - + -
450B THR 5.7 0.7 - - - +
451B PHE* 4.0 16.6 - - + -
454B TYR* 3.2 47.6 - - + +
520B TYR* 2.5 54.2 + - + -
529B LYS* 5.4 2.0 - - + -
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Residues in contact with MET 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B CYS 3.1 22.0 + - - +
379B LEU 3.2 0.6 - - - -
380B MET* 1.3 101.4 - - + +
382B GLU* 1.3 61.9 + - - +
383B PRO* 3.3 2.9 - - - -
384B THR* 2.8 29.3 + - + -
385B ALA* 3.8 1.7 + - - +
406B THR* 5.4 0.5 - - - +
409B ILE* 3.5 16.8 - - + +
451B PHE* 4.7 13.2 - - + -
454B TYR* 4.2 18.8 - - + -
520B TYR* 4.5 4.9 - - - +
547B VAL* 4.8 3.6 - - + -
548B VAL* 4.0 21.3 - - + -
551B THR* 3.5 37.5 - - + +
552B CYS* 3.8 23.5 - - - -
677B ILE* 4.3 2.0 - - + -
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLY 4.6 1.2 - - - +
161B PHE* 3.6 12.6 - - - +
162B VAL* 3.0 30.0 + - - +
378B HIS 3.4 5.5 + - - +
379B LEU* 3.8 6.0 - - - +
381B MET* 1.3 75.0 - - - +
383B PRO* 1.3 72.1 - - + +
385B ALA* 2.9 15.2 + - - +
386B VAL* 3.2 13.6 + - + +
409B ILE* 3.8 10.8 - - + -
410B MET* 4.3 19.2 - - + +
413B ASN* 2.9 34.1 + - - +
417B ARG* 3.0 32.7 + - - -
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Residues in contact with PRO 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 3.6 15.4 - - + -
159B PRO* 4.0 1.6 - - + -
160B GLY 3.5 13.7 - - - +
379B LEU 3.1 16.6 - - - +
380B MET 3.5 3.8 - - - +
381B MET 3.3 4.5 - - - -
382B GLU* 1.3 93.2 - - + +
384B THR* 1.3 54.5 - - - +
386B VAL* 3.4 0.8 + - + -
387B SER* 2.9 24.8 + - - -
515B LEU* 3.2 12.3 - - + +
519B GLY* 3.5 35.7 - - - +
520B TYR* 3.7 25.8 - - + +
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET* 2.8 22.7 + - + +
383B PRO* 1.3 74.1 - - - +
385B ALA* 1.3 58.1 + - - +
387B SER* 4.6 0.2 - - - -
388B SER* 2.7 34.0 + - - -
402B LEU* 5.4 0.7 - - - -
406B THR* 3.9 16.5 - - - +
451B PHE* 6.1 0.2 - - + -
511B TRP* 3.6 14.5 + - - -
515B LEU* 3.9 19.5 - - + -
520B TYR* 3.6 19.3 - - - +
544B PHE* 4.7 5.6 - - + -
548B VAL* 4.0 33.2 - - + +
552B CYS* 5.3 0.2 - - - -
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET 4.7 0.2 - - - +
382B GLU* 2.9 10.4 + - - +
384B THR* 1.3 80.4 + - - +
386B VAL* 1.3 65.1 + - - +
388B SER* 3.3 12.8 + - - -
389B TRP* 3.2 24.1 + - + +
406B THR* 4.0 20.2 - - + +
409B ILE* 3.6 28.0 - - + -
410B MET* 4.4 15.9 - - + -
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 4.4 10.1 - - + +
147B LYS 4.4 7.9 - - - +
148B TRP* 3.7 32.5 - - + -
161B PHE 4.3 0.7 - - - -
162B VAL* 3.8 35.7 - - + +
382B GLU* 3.2 16.5 + - + +
383B PRO 3.8 1.1 - - - +
385B ALA* 1.3 76.6 - - - +
387B SER* 1.3 62.0 + - - +
389B TRP* 3.3 6.7 + - - +
390B ARG* 3.2 41.6 + - + +
410B MET* 4.1 11.7 - - - -
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 4.3 3.8 - - - -
383B PRO 2.9 18.5 + - - -
386B VAL* 1.3 73.3 - - - +
388B SER* 1.3 66.3 + - - +
391B ASN* 2.9 39.5 + - - +
511B TRP* 2.9 42.4 + - - -
514B ASP* 3.7 10.0 - - - +
515B LEU* 3.5 17.7 - - - -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR 2.7 19.6 + - - -
385B ALA* 3.4 12.6 - - - -
386B VAL 3.2 0.2 - - - -
387B SER* 1.3 77.0 - - - +
389B TRP* 1.3 57.1 + - - +
392B LEU* 3.0 43.1 + - - +
399B TRP* 3.7 22.9 - - - -
402B LEU* 4.2 17.2 - - - +
406B THR* 5.4 4.6 + - - +
511B TRP* 3.5 15.2 + - - +
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Residues in contact with TRP 389 (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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106B ARG* 3.9 33.4 - - - -
139B VAL* 4.6 1.6 - - - +
142B ASN* 3.0 50.7 + - - +
146B TYR* 3.3 50.9 - + + -
173B ASP* 4.3 12.8 - - + -
174B VAL* 3.5 22.9 - - + +
385B ALA* 3.2 23.0 + - - +
386B VAL* 3.3 6.3 + - - +
387B SER 3.3 0.4 - - - -
388B SER* 1.3 79.8 - - - +
390B ARG* 1.3 60.4 + - - +
391B ASN 3.8 0.2 + - - -
392B LEU 4.5 2.5 - - - +
399B TRP* 3.6 35.2 - + - -
403B TYR* 4.7 12.0 - + - -
410B MET* 3.4 28.0 - - + +
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Residues in contact with ARG 390 (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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139B VAL* 3.1 7.4 - - - +
143B LYS* 2.7 67.0 + - + +
146B TYR* 3.1 37.8 + - + +
147B LYS* 3.3 31.9 - - - +
148B TRP* 3.3 22.7 - - - +
386B VAL* 3.2 30.8 + - - +
388B SER 3.2 0.4 - - - -
389B TRP* 1.3 80.1 - - - +
391B ASN* 1.3 65.1 + - - +
514B ASP* 2.9 24.4 + - - -
518B ASN* 5.5 1.0 - - - +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 3.9 13.1 - - - +
143B LYS* 4.0 11.4 + - - +
387B SER* 2.9 33.1 + - - +
390B ARG* 1.3 86.5 - - - +
392B LEU* 1.3 65.4 - - - +
393B PRO* 3.9 5.5 - - - +
507B GLU* 3.7 13.6 - - - +
510B ASP* 3.4 32.6 - - + +
511B TRP* 3.6 20.2 - - + +
514B ASP* 3.1 30.4 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 3.7 6.5 - - - +
142B ASN* 4.8 5.5 + - - -
388B SER* 3.0 26.7 + - - +
389B TRP 4.5 4.3 - - - +
391B ASN* 1.3 79.9 - - - +
393B PRO* 1.3 66.9 - - + +
394B SER 4.1 0.3 + - - -
396B HIS* 3.9 20.6 - - + +
398B VAL* 4.1 25.4 - - + -
399B TRP* 4.1 33.6 - - + +
402B LEU* 5.5 0.2 - - + -
507B GLU* 3.5 31.4 - - + +
508B ILE* 4.2 3.6 - - + +
511B TRP* 4.0 32.3 - - + +
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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
------------------------------------------------------------
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