Contacts of the helix formed by residues 436 - 447 (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 GLY 436 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299B PRO* 5.3 2.0 - - - -
423B THR* 4.2 9.6 - - - +
428B ASP* 3.9 1.0 + - - -
435B GLY* 1.3 80.8 - - - +
437B GLY* 1.3 63.9 + - - +
438B GLN* 2.9 15.2 + - - -
439B VAL* 3.4 16.0 + - - +
440B THR* 3.4 13.1 + - - -
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Residues in contact with GLY 437 (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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298B ILE* 3.7 14.3 - - - +
299B PRO* 3.9 24.0 + - - +
433B ILE* 3.1 15.5 + - - -
435B GLY 3.7 1.6 - - - -
436B GLY* 1.3 75.8 - - - +
438B GLN* 1.3 58.4 + - - +
440B THR* 3.1 8.9 + - - -
441B LEU* 2.9 31.2 + - - +
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Residues in contact with GLN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B MET* 3.3 42.2 - - + +
421B ILE 3.0 28.3 + - - +
422B PRO 3.7 10.5 + - - -
423B THR* 4.2 1.6 - - - +
427B ALA* 4.7 5.4 - - + -
428B ASP* 3.1 29.0 + - - +
431B LEU* 4.6 4.7 - - + -
433B ILE* 3.1 26.6 + - + +
434B GLY* 3.5 4.2 - - - -
435B GLY 3.5 2.4 + - - -
436B GLY* 2.9 25.3 + - - +
437B GLY* 1.3 73.6 + - - +
439B VAL* 1.3 65.3 + - + +
441B LEU* 3.7 3.8 + - - +
442B MET* 3.5 13.5 + - - +
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Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG 4.8 9.4 - - - +
154B TYR* 5.0 5.8 - - + -
158B LEU* 4.8 8.3 - - + -
421B ILE* 3.6 37.0 - - + +
422B PRO* 5.2 3.1 - - + -
436B GLY* 3.4 9.5 + - - +
437B GLY 3.2 0.2 - - - -
438B GLN* 1.3 78.3 - - + +
440B THR* 1.3 67.2 + - - +
441B LEU 3.2 0.2 - - - -
442B MET* 3.2 17.1 + - + +
443B GLN* 3.0 42.0 + - + +
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Residues in contact with THR 440 (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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297B GLY 5.6 0.9 - - - +
298B ILE* 3.9 17.3 - - + -
299B PRO* 5.1 9.2 - - + +
436B GLY 3.4 12.2 + - - -
437B GLY* 3.1 12.7 + - - -
439B VAL* 1.3 80.5 - - - +
441B LEU* 1.3 56.4 + - - +
443B GLN* 3.4 16.4 + - + +
444B LYS* 2.9 28.5 + - + +
447B ARG* 5.1 5.3 + - - +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 4.0 33.0 - - + +
295B LEU* 4.1 15.7 - - + -
298B ILE* 4.1 11.6 - - + +
366B GLN 3.7 24.2 - - - +
367B TYR* 4.5 1.3 - - - +
370B MET* 4.0 7.0 - - + -
371B ILE* 3.8 24.8 - - + +
433B ILE* 3.6 24.5 - - + -
437B GLY 2.9 15.9 + - - +
438B GLN 3.8 5.4 - - - +
439B VAL 3.2 0.2 - - - -
440B THR* 1.3 76.2 - - - +
442B MET* 1.3 64.3 + - - +
444B LYS* 3.3 2.0 + - - +
445B HIS* 3.2 20.1 + - - +
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Residues in contact with MET 442 (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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154B TYR* 5.6 0.4 - - + -
158B LEU* 4.1 16.8 - - + -
370B MET* 3.4 44.4 - - + +
371B ILE* 4.8 2.2 - - - -
374B LEU* 4.3 5.2 - - - -
375B LEU* 3.5 24.8 - - + +
379B LEU* 3.9 29.4 - - + -
421B ILE* 3.6 31.9 - - + -
438B GLN 3.5 10.1 + - - +
439B VAL* 3.2 19.2 + - + +
441B LEU* 1.3 74.7 - - - +
443B GLN* 1.3 65.6 + - - +
445B HIS* 3.2 2.7 + - - -
446B TYR* 2.9 21.1 + - - +
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Residues in contact with GLN 443 (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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153B ARG 5.0 5.9 + - - -
156B GLN* 3.0 38.3 + - - +
157B ASP* 3.4 22.9 - - + +
158B LEU* 4.2 10.6 - - + +
439B VAL* 3.0 28.8 + - + +
440B THR* 3.6 24.7 + - + +
442B MET* 1.3 76.0 - - - +
444B LYS* 1.3 61.6 + - - +
446B TYR* 3.8 0.5 - - - +
447B ARG* 3.1 39.8 + - - +
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Residues in contact with LYS 444 (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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293B LYS 4.2 2.4 + - - -
294B ILE* 2.9 43.2 + - + +
296B GLU* 2.6 32.5 + - - +
298B ILE* 4.2 11.4 - - + -
440B THR* 2.9 18.8 + - + +
441B LEU* 3.6 6.7 - - - +
442B MET 3.1 0.2 - - - -
443B GLN* 1.3 78.7 - - - +
445B HIS* 1.3 62.3 + - - +
447B ARG* 3.6 34.7 + - - +
448B SER* 4.1 8.7 + - - -
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Residues in contact with HIS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 4.0 12.5 - - + +
367B TYR* 4.1 12.5 + - - -
371B ILE* 3.8 43.3 - - + +
375B LEU* 3.5 21.3 - - + -
376B ARG* 3.2 34.9 + - + -
441B LEU 3.2 2.9 + - - +
442B MET 3.2 7.0 + - - +
444B LYS* 1.3 78.5 - - - +
446B TYR* 1.3 63.6 + - - +
448B SER* 3.2 7.2 + - - -
449B VAL* 3.1 31.1 + - + +
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Residues in contact with TYR 446 (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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157B ASP* 3.3 34.3 - - - +
158B LEU* 3.6 17.6 + - - -
159B PRO* 3.5 31.4 - - + +
375B LEU* 4.4 9.9 - - + -
380B MET* 3.8 14.1 - - - -
442B MET 2.9 13.9 + - - +
443B GLN 3.8 0.4 - - - +
444B LYS 3.4 0.2 - - - -
445B HIS* 1.3 77.9 - - - +
447B ARG* 1.3 66.1 + - - +
448B SER 2.9 1.6 + - - -
449B VAL* 3.0 25.9 + - + +
520B TYR* 3.2 24.8 - + - -
521B PRO* 2.8 33.0 + - + +
522B ALA 4.6 3.6 - - - -
523B GLY* 4.7 1.3 - - - -
529B LYS* 3.1 34.3 + - + -
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Residues in contact with ARG 447 (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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157B ASP* 2.9 36.4 + - - +
440B THR* 5.1 6.5 + - - +
443B GLN* 3.1 32.9 + - - +
444B LYS* 3.6 35.9 + - - +
445B HIS 3.3 0.4 - - - -
446B TYR* 1.3 79.0 - - - +
448B SER* 1.3 57.5 + - - +
522B ALA 4.3 4.8 - - - +
523B GLY* 5.3 0.2 - - - -
524B SER* 3.1 25.7 + - - +
525B ASP* 3.5 32.4 + - + +
527B THR* 3.0 28.2 + - - -
529B LYS* 3.9 3.2 + - - +
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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