Contacts of the helix formed by residues 528 - 539 (chain B) in PDB entry 3V42
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 PRO 528 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527B ARG* 1.3 106.4 - - + +
529B LYS* 1.3 70.7 + - - +
530B GLU* 3.0 5.4 + - + +
531B ASP* 3.1 25.0 + - - +
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Residues in contact with LYS 529 (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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527B ARG 3.3 6.4 + - - +
528B PRO* 1.3 71.8 - - - +
530B GLU* 1.3 63.6 + - - +
532B THR* 3.0 24.2 + - - -
533B GLN* 4.0 1.9 + - - +
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Residues in contact with GLU 530 (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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528B PRO* 3.0 4.6 + - + -
529B LYS* 1.3 79.3 - - - +
531B ASP* 1.3 65.4 + - - +
532B THR 3.2 0.5 + - - -
533B GLN* 3.3 9.4 + - - +
534B LYS* 3.3 19.1 + - - +
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Residues in contact with ASP 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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521B PHE* 3.8 10.4 - - + -
527B ARG* 3.4 33.8 + - + +
528B PRO* 3.1 18.7 + - - +
529B LYS 3.1 0.2 + - - -
530B GLU* 1.3 79.8 - - - +
532B THR* 1.3 62.9 + - - +
534B LYS* 3.3 9.0 + - - +
535B LEU* 3.0 24.1 + - - +
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Residues in contact with THR 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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518B LEU* 4.1 22.7 - - + -
521B PHE* 3.6 13.3 - - - -
522B THR* 3.4 23.8 - - + +
527B ARG* 4.0 6.4 - - - +
529B LYS* 3.0 14.4 + - - -
531B ASP* 1.3 76.6 - - - +
533B GLN* 1.3 65.5 + - - +
535B LEU* 3.4 3.3 + - - +
536B LEU* 3.0 35.0 + - + +
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Residues in contact with GLN 533 (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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529B LYS 4.0 1.4 + - - +
530B GLU* 3.3 11.8 + - - +
532B THR* 1.3 80.4 - - - +
534B LYS* 1.3 58.0 + - - +
536B LEU* 3.2 12.1 + - + +
537B SER* 2.8 31.1 + - - -
542B SER* 4.6 5.1 - - - -
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Residues in contact with LYS 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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530B GLU 3.3 10.0 + - - +
531B ASP* 3.3 13.2 + - - +
532B THR 3.2 0.8 - - - -
533B GLN* 1.3 78.5 - - - +
535B LEU* 1.3 61.1 + - - +
537B SER* 3.4 7.1 + - - -
538B ILE* 3.3 28.6 + - + +
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Residues in contact with LEU 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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517B VAL* 4.4 16.6 - - + +
518B LEU* 5.2 8.3 - - + -
521B PHE* 3.5 49.1 - - + -
531B ASP 3.0 15.9 + - - +
532B THR 3.7 4.3 - - - +
534B LYS* 1.3 72.1 - - - +
536B LEU* 1.3 67.9 + - + +
538B ILE* 3.1 25.8 + - + +
539B LEU* 3.2 30.9 + - + +
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Residues in contact with LEU 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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518B LEU* 4.0 27.4 - - + -
532B THR* 3.0 28.9 + - + +
533B GLN* 3.3 14.4 - - - +
535B LEU* 1.3 80.5 - - + +
537B SER* 1.3 61.8 + - - +
539B LEU* 3.2 14.9 + - + -
541B ALA* 2.8 47.3 + - + +
542B SER* 4.0 6.5 - - - +
547B VAL* 3.7 21.5 - - + -
550B LEU* 4.3 20.4 - - + -
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Residues in contact with SER 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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533B GLN 2.8 16.5 + - - -
534B LYS* 3.8 7.8 + - - -
535B LEU 3.2 0.2 - - - -
536B LEU* 1.3 77.0 - - - +
538B ILE* 1.3 63.2 + - - +
540B GLY* 3.2 12.7 + - - +
542B SER* 3.9 22.2 - - - +
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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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534B LYS* 3.3 17.4 + - + +
535B LEU* 3.1 17.6 + - + +
537B SER* 1.3 80.5 - - - +
539B LEU* 1.3 65.3 + - + +
540B GLY 3.2 3.0 + - - -
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Residues in contact with LEU 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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514B LYS* 2.9 59.2 + - + +
517B VAL* 4.0 27.4 - - + -
518B LEU* 6.5 0.4 - - + -
535B LEU* 3.2 29.4 + - + +
536B LEU* 3.2 11.3 + - + +
538B ILE* 1.3 84.9 - - + +
540B GLY* 1.3 62.5 + - - +
541B ALA* 3.4 3.8 + - + +
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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