Contacts of the helix formed by residues 530 - 539 (chain B) in PDB entry 3V4R
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 SER 530 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525B GLU* 4.8 3.6 - - - -
526B GLY 3.5 3.9 + - - -
527B PHE* 2.7 27.9 + - - -
528B LEU 3.6 0.4 - - - -
529B ARG* 1.4 81.2 - - - +
531B GLU* 1.4 67.2 + - - +
532B ARG* 4.0 5.9 + - - +
533B SER* 3.3 15.1 + - - -
534B LEU* 3.0 21.2 + - - +
559B SER* 4.0 6.7 - - - -
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Residues in contact with GLU 531 (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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530B SER* 1.4 72.1 - - - +
532B ARG* 1.3 71.1 + - - +
534B LEU* 3.4 3.6 + - - +
535B ILE* 3.2 28.7 + - + +
559B SER* 3.6 30.6 + - - +
562B ILE* 4.1 31.2 - - + -
563B ALA* 4.2 0.7 - - - +
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Residues in contact with ARG 532 (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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341B HIS* 3.7 24.5 - - + -
395B THR* 3.2 40.2 + - - +
396B PRO 3.0 30.1 + - - -
397B GLY* 3.6 13.5 - - - -
398B PRO* 3.6 19.3 - - - +
401B ILE* 4.0 8.7 - - - +
530B SER* 3.3 6.8 + - - +
531B GLU* 1.3 81.3 - - - +
533B SER* 1.3 66.2 + - - +
535B ILE* 2.9 16.2 + - + +
536B GLN* 3.0 13.4 + - - +
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Residues in contact with SER 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LEU* 3.9 15.5 - - - +
527B PHE* 3.0 40.3 + - - -
528B LEU* 3.6 22.8 - - - +
530B SER* 3.2 14.7 + - - -
532B ARG* 1.3 75.9 - - - +
534B LEU* 1.4 53.9 + - - +
536B GLN* 3.2 6.4 + - - +
537B THR* 2.7 36.3 + - - -
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Residues in contact with LEU 534 (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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519B ILE* 4.1 33.2 - - + -
522B ALA 4.6 3.4 - - - +
528B LEU 4.3 3.1 - - - +
529B ARG* 3.5 35.9 - - - +
530B SER 3.0 15.9 + - - +
531B GLU 3.6 4.0 - - - +
533B SER* 1.4 76.0 - - - +
535B ILE* 1.3 57.1 + - - +
537B THR* 3.1 6.6 + - - +
538B ILE* 2.9 38.6 + - + +
551B MET* 4.7 7.2 - - + -
559B SER 4.1 4.0 - - - +
560B MET* 3.9 41.5 - - + +
563B ALA* 3.9 10.3 - - + -
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Residues in contact with ILE 535 (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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394B ALA* 5.9 1.3 - - + -
395B THR* 3.5 31.2 - - + -
531B GLU* 3.2 20.3 + - + +
532B ARG* 2.9 9.1 + - + +
534B LEU* 1.3 73.4 - - - +
536B GLN* 1.4 61.0 + - - +
538B ILE* 3.5 10.1 + - + +
539B GLY* 3.2 17.8 + - - -
562B ILE* 4.8 7.9 - - + -
563B ALA* 3.8 29.2 - - - +
566B GLU* 4.2 20.4 - - + -
567B THR* 5.2 6.3 - - - +
570B ARG* 4.2 19.3 - - - +
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Residues in contact with GLN 536 (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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341B HIS* 5.8 5.4 - - - +
395B THR* 5.2 4.2 - - + +
505B LEU* 3.6 24.0 - - + -
532B ARG 3.0 11.5 + - - +
533B SER* 3.6 5.4 - - - +
535B ILE* 1.4 72.2 - - - +
537B THR* 1.4 65.5 + - - +
539B GLY* 3.2 14.5 + - - -
540B ARG* 3.6 15.7 + - - +
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Residues in contact with THR 537 (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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451B THR* 4.0 13.9 - - + -
504B LEU* 5.0 11.2 - - + +
505B LEU* 3.5 16.4 - - - +
517B VAL* 3.9 19.4 - - + +
519B ILE* 3.9 26.5 - - + -
528B LEU* 4.7 6.2 + - - +
529B ARG* 5.5 2.6 + - - +
533B SER 2.7 22.0 + - - -
534B LEU* 3.1 11.6 + - + +
536B GLN* 1.4 72.6 - - - +
538B ILE* 1.4 64.2 + - - +
540B ARG* 3.2 23.3 + - + +
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Residues in contact with ILE 538 (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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419B ASP* 5.3 2.7 - - - +
420B PRO* 3.4 35.1 - - + +
422B ILE* 3.8 22.0 - - + -
519B ILE* 4.6 2.7 - - + -
534B LEU 2.9 27.4 + - - +
535B ILE* 3.6 9.0 - - + +
537B THR* 1.4 74.4 - - - +
539B GLY* 1.3 57.3 + - - +
540B ARG 3.0 6.3 + - - -
541B ALA* 3.1 15.4 + - - +
549B VAL* 4.0 20.9 - - + -
551B MET* 3.8 22.7 - - + -
563B ALA* 4.0 13.2 - - + -
567B THR* 4.0 24.7 - - + +
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Residues in contact with GLY 539 (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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41B THR* 4.7 13.3 + - - -
413B ARG* 6.1 0.4 - - - -
419B ASP* 4.9 6.1 - - - -
510B ASP* 4.2 9.5 - - - +
535B ILE 3.2 13.7 + - - -
536B GLN* 3.2 8.8 + - - -
538B ILE* 1.3 76.1 - - - +
540B ARG* 1.3 59.9 + - - +
541B ALA 3.1 2.2 + - - -
542B ALA* 3.3 23.3 + - - +
543B ARG* 4.6 1.9 + - - +
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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