Contacts of the helix formed by residues 413 - 432 (chain A) in PDB entry 2VGB
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 PHE 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A MET* 3.5 27.4 + - + +
379A THR 3.9 11.7 - - - -
380A LYS* 3.5 22.2 - - - +
381A PRO* 4.0 29.8 - - + -
407A GLU 4.1 4.0 - - - -
411A GLY* 3.2 1.6 - - - -
412A ASN* 1.3 100.0 - - + +
414A PRO* 1.4 57.1 - - - +
416A GLU* 3.2 40.6 + - + +
417A ALA* 2.8 32.7 + - - +
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Residues in contact with PRO 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 3.8 23.6 - - + +
103A ARG* 4.3 16.8 - - + +
107A MET* 4.5 10.3 - - - -
407A GLU 3.4 12.5 - - - +
408A THR* 3.7 30.8 - - + +
411A GLY 3.6 8.5 - - - +
412A ASN 3.5 6.7 - - - +
413A PHE* 1.4 89.0 - - - +
415A VAL* 1.3 63.4 + - + +
416A GLU* 4.5 1.3 - - - +
417A ALA* 3.4 3.7 + - + +
418A VAL* 3.1 28.5 + - - +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 4.5 19.3 - - + +
106A GLU* 3.8 34.5 - - + +
107A MET* 3.7 24.2 - - + -
110A ALA* 4.2 12.6 - - + -
413A PHE 3.4 0.2 - - - -
414A PRO* 1.3 75.7 - - + +
416A GLU* 1.3 74.8 + - - +
418A VAL* 3.0 5.1 + - - +
419A LYS* 2.9 44.8 + - - +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A MET* 3.9 18.5 - - + +
381A PRO* 4.8 6.3 - - + +
412A ASN 4.5 0.2 - - - +
413A PHE* 3.2 45.6 - - + +
414A PRO* 4.5 1.0 - - - +
415A VAL* 1.3 81.2 + - + +
417A ALA* 1.3 62.8 + - - +
419A LYS* 3.1 15.7 + - + +
420A MET* 2.9 23.2 + - - +
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU* 3.6 10.9 - - + +
377A MET* 3.9 22.4 - - + +
404A LEU* 4.1 11.0 - - + -
407A GLU* 3.8 30.5 - - + +
413A PHE 2.8 20.8 + - - +
414A PRO 3.5 7.4 - - - +
415A VAL 3.2 0.2 - - - -
416A GLU* 1.3 72.4 - - - +
418A VAL* 1.3 62.0 + - - +
420A MET 3.3 0.9 + - - -
421A GLN* 3.2 20.4 + - - +
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 3.9 10.4 - - + +
92A ALA* 4.5 5.8 - - + -
107A MET* 4.0 21.8 - - + +
110A ALA* 3.9 7.0 - - + +
111A GLY* 3.9 14.6 - - - +
112A MET* 3.7 28.3 - - + +
404A LEU* 3.7 20.6 - - + -
408A THR* 3.8 9.4 - - + -
414A PRO 3.1 13.5 + - - +
415A VAL* 3.0 8.5 + - - +
417A ALA* 1.3 73.4 - - - +
419A LYS* 1.3 67.3 + - - +
421A GLN* 3.3 3.2 + - - -
422A HIS* 3.0 20.8 + - - +
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Residues in contact with LYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 3.7 21.3 - - + +
415A VAL* 2.9 34.0 + - - +
416A GLU* 3.5 16.8 - - + +
418A VAL* 1.3 76.5 - - - +
420A MET* 1.3 56.3 + - - +
422A HIS* 3.4 11.6 + - - +
423A ALA* 2.9 28.1 + - - +
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Residues in contact with MET 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU* 4.0 11.2 - - + -
377A MET* 4.3 7.2 - - + -
382A ARG* 4.5 12.3 - - - -
383A PRO* 3.8 31.6 - - + -
388A THR* 4.1 6.5 - - - +
416A GLU 2.9 12.0 + - - +
417A ALA 3.7 7.4 - - - +
418A VAL 3.2 0.4 - - - -
419A LYS* 1.3 73.1 - - - +
421A GLN* 1.3 67.8 + - - +
422A HIS 3.0 0.9 - - - -
423A ALA* 2.9 13.7 + - + +
424A ILE* 3.0 52.0 + - + +
346C ALA* 4.4 2.5 - - + -
347C GLU* 3.6 37.9 - - + +
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Residues in contact with GLN 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 3.4 35.9 - - + +
373A MET* 3.9 20.1 - - - +
374A LEU* 3.6 17.9 - - + -
391A VAL* 4.4 10.8 - - + +
402A ILE* 3.4 35.9 + - + +
403A MET 3.0 17.0 + - - +
404A LEU* 3.4 21.5 - - + +
417A ALA 3.2 6.8 + - - +
418A VAL 3.3 2.7 + - - +
420A MET* 1.3 76.3 - - - +
422A HIS* 1.3 64.0 + - - +
424A ILE* 4.2 1.1 - - - +
425A ALA* 3.0 27.9 + - - +
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Residues in contact with HIS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA* 6.2 0.2 - - - -
86A ARG* 2.9 52.6 + - + +
90A ILE* 3.6 5.9 - - + +
110A ALA 3.8 18.0 + - - +
111A GLY* 5.1 0.6 - - - -
418A VAL 3.0 13.6 + - - +
419A LYS* 3.5 10.5 - - - +
421A GLN* 1.3 81.4 - - - +
423A ALA* 1.3 67.0 + - + +
426A ARG* 3.3 45.8 + - - +
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Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A LYS 2.9 15.9 + - - +
420A MET* 2.9 9.3 + - + +
422A HIS* 1.3 85.1 - - + +
424A ILE* 1.3 64.2 + - - +
426A ARG* 3.5 6.3 + - - +
427A GLU* 3.5 22.0 + - - +
347C GLU* 3.2 29.9 - - + +
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Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU* 4.5 1.8 - - + -
388A THR* 3.8 22.7 - - + +
391A VAL* 3.7 31.4 - - + -
392A ALA* 3.5 38.8 - - + +
420A MET* 3.0 48.8 + - + +
423A ALA* 1.3 75.0 - - - +
425A ALA* 1.3 68.1 + - - +
426A ARG 3.0 0.7 + - - -
427A GLU* 3.0 5.1 + - - +
428A ALA* 2.9 20.6 + - - +
347C GLU* 4.5 11.4 - - - +
350C PHE* 4.5 8.3 - - + -
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 4.3 10.8 - - - +
88A THR* 4.1 13.2 - - - -
391A VAL* 4.5 1.0 - - - +
395A VAL* 4.2 15.3 - - + -
402A ILE* 4.4 8.1 - - + -
421A GLN 3.0 19.9 + - - +
422A HIS 4.0 2.2 - - - +
424A ILE* 1.3 76.7 - - - +
426A ARG* 1.3 57.0 + - - +
428A ALA* 3.9 1.3 - - - +
429A GLU* 2.8 53.6 + - - +
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Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO* 3.8 42.5 + - + +
83A VAL* 4.4 0.4 - - - +
84A ALA 3.0 37.8 + - - +
85A ALA* 5.0 0.4 - - - +
86A ARG* 3.2 25.1 - - + +
422A HIS* 3.3 39.2 + - + +
423A ALA* 3.8 6.5 + - - +
424A ILE 3.0 1.0 + - - -
425A ALA* 1.3 78.1 - - - +
427A GLU* 1.3 62.9 + - - +
429A GLU* 3.6 7.1 + - - +
430A ALA* 3.3 20.3 + - - +
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Residues in contact with GLU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 4.6 3.5 + - - +
80A SER 4.4 3.3 - - - +
81A GLU* 4.1 0.3 - - - +
82A PRO* 3.2 25.7 - - + +
423A ALA 3.5 14.3 - - - +
424A ILE 3.0 5.8 + - - +
426A ARG* 1.3 77.1 - - - +
428A ALA* 1.3 62.6 + - - +
430A ALA* 3.3 8.4 + - - +
431A ALA* 3.2 19.8 + - - +
347C GLU* 3.7 22.4 - - + +
348C LYS* 3.0 42.8 + - - +
350C PHE* 3.6 20.3 - - + -
351C LEU* 3.6 12.0 - - + +
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ALA* 3.8 27.6 - - + +
395A VAL* 3.6 28.0 - - + -
396A LEU* 3.4 10.3 - - + +
424A ILE 2.9 18.3 + - - +
425A ALA* 3.9 1.1 - - - +
427A GLU* 1.3 72.0 - - - +
429A GLU* 1.3 58.3 + - - +
431A ALA* 2.8 17.9 + - - -
432A VAL* 3.2 9.5 + - - +
350C PHE* 3.6 12.5 - - + -
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Residues in contact with GLU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA 4.2 1.6 - - - +
86A ARG* 3.1 11.7 - - - +
87A SER* 2.7 41.8 + - - +
88A THR* 2.5 35.3 + - - +
395A VAL* 3.8 14.8 - - + -
425A ALA* 2.8 30.0 + - - +
426A ARG* 4.0 4.5 - - - +
428A ALA* 1.3 76.6 - - - +
430A ALA* 1.3 60.4 + - - +
431A ALA 3.3 0.7 + - - -
432A VAL* 3.4 20.5 + - - +
434A HIS* 3.9 11.3 + - - -
490A ARG* 4.1 0.7 + - - -
510A ARG* 4.9 6.7 - - - +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN* 3.8 23.6 - - + +
60A GLN* 3.2 27.7 - - + +
72A HIS* 5.5 0.7 - - - -
80A SER 6.0 0.4 - - - +
82A PRO* 4.8 10.8 - - + -
83A VAL 5.8 0.2 - - - +
426A ARG 3.3 10.3 + - - +
427A GLU* 3.3 11.9 + - - +
429A GLU* 1.3 75.9 - - - +
431A ALA* 1.3 57.9 + - - +
432A VAL 3.5 0.9 - - - +
490A ARG* 3.1 24.2 + - - +
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 4.7 0.2 - - + -
72A HIS* 2.8 29.1 + - - -
76A LEU* 3.8 29.6 - - + -
396A LEU* 4.0 12.7 - - + +
427A GLU 3.2 10.5 + - - +
428A ALA* 2.8 14.6 + - - +
430A ALA* 1.3 76.2 - - - +
432A VAL* 1.3 59.7 + - - +
433A TYR 3.3 0.3 + - - -
350C PHE* 4.5 3.6 - - + -
351C LEU* 4.0 14.4 - - + -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 5.5 2.8 - - - +
72A HIS* 4.1 3.3 - - - -
395A VAL* 4.6 5.6 - - + +
396A LEU* 3.9 16.8 - - + +
428A ALA 3.2 8.2 + - - +
429A GLU* 3.4 21.2 + - - +
430A ALA 4.3 0.5 - - - +
431A ALA* 1.3 77.6 - - - +
433A TYR* 1.3 63.3 + - - +
434A HIS* 3.1 46.6 + - + +
437A LEU* 3.6 25.4 - - + -
490A ARG* 4.0 4.7 + - - -
510A ARG* 4.1 22.0 - - - +
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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