Contacts of the helix formed by residues 615 - 629 (chain B) in PDB entry 4CCN
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 615 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613B CYS 3.8 0.8 - - - -
614B ASP* 1.3 77.9 - - - +
616B VAL* 1.3 70.1 + - - +
617B GLU* 3.0 16.6 + - - +
618B ASP* 2.8 35.5 + - - +
619B GLN* 3.2 18.3 + - - +
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Residues in contact with VAL 616 (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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544B THR* 3.6 28.7 - - + -
615B SER* 1.3 77.6 + - - +
617B GLU* 1.3 62.0 + - - +
619B GLN* 3.7 16.5 - - - +
620B LEU* 3.1 35.5 + - + +
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Residues in contact with GLU 617 (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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615B SER* 3.0 13.0 + - - +
616B VAL* 1.3 80.7 - - - +
618B ASP* 1.3 57.7 - - - +
620B LEU* 4.4 4.3 - - - +
621B SER* 2.9 28.9 + - - -
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Residues in contact with ASP 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B GLN* 4.2 20.8 - - - +
591B GLN* 3.6 12.5 + - + +
613B CYS* 3.7 19.5 - - + -
614B ASP* 3.6 12.8 - - - +
615B SER* 2.8 38.6 + - - +
617B GLU* 1.3 79.3 - - - +
619B GLN* 1.3 65.5 + - - +
621B SER* 3.3 5.3 - - - -
622B LEU* 3.0 24.9 + - - +
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Residues in contact with GLN 619 (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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544B THR* 4.4 4.4 - - + +
608B VAL* 3.2 33.4 - - + +
609B GLY* 2.7 34.5 + - - +
611B LEU* 2.6 38.3 + - + +
613B CYS* 3.8 18.3 - - + +
615B SER 3.2 13.8 + - - +
616B VAL* 3.4 25.0 + - - +
618B ASP* 1.3 77.0 - - - +
620B LEU* 1.3 62.7 + - + +
622B LEU* 5.2 0.2 - - - -
623B ALA* 3.3 14.9 + - - +
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Residues in contact with LEU 620 (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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542B LEU* 4.5 11.9 - - + +
543B THR* 3.8 10.5 - - - +
544B THR* 3.7 37.2 - - + +
608B VAL* 4.0 10.5 - - + -
616B VAL* 3.1 30.9 + - + +
617B GLU* 4.4 3.8 - - - +
619B GLN* 1.3 73.1 - - - +
621B SER* 1.3 60.4 + - - +
623B ALA* 4.5 1.3 - - - -
624B THR* 2.6 41.9 + - - +
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Residues in contact with SER 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B GLN* 2.8 17.8 + - - -
617B GLU 2.9 23.1 + - - -
618B ASP* 3.2 8.7 + - - -
620B LEU* 1.3 77.4 - - - +
622B LEU* 1.3 56.5 + - - +
624B THR* 3.8 3.4 - - - -
625B THR* 2.9 37.4 + - - -
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Residues in contact with LEU 622 (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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585B LEU* 5.9 0.7 - - + -
587B ILE* 4.0 26.0 - - + -
591B GLN* 3.4 30.5 - - + +
594B ALA* 3.8 29.6 - - + -
595B MET* 3.9 18.2 - - - +
598B LEU* 4.4 9.2 - - + -
611B LEU* 5.0 3.6 - - + -
613B CYS* 5.4 0.9 - - - -
618B ASP 3.0 9.3 + - - +
619B GLN* 4.3 2.9 - - - +
621B SER* 1.3 78.4 + - - +
623B ALA* 1.3 55.9 + - - +
625B THR* 3.1 8.7 + - + -
626B LEU* 2.8 60.5 + - + +
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Residues in contact with ALA 623 (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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542B LEU* 3.8 12.9 - - + +
548B VAL* 5.3 0.9 - - + -
608B VAL* 3.8 28.5 - - + -
611B LEU* 4.6 5.3 - - + +
619B GLN 3.3 18.2 + - - +
620B LEU* 3.9 2.7 - - - +
622B LEU* 1.3 79.5 - - - +
624B THR* 1.3 57.9 + - - +
626B LEU* 4.7 1.1 - - - -
627B TYR* 2.9 32.1 + - - +
632B LEU* 3.8 17.0 - - + +
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Residues in contact with THR 624 (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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542B LEU* 4.5 23.0 + - + +
620B LEU* 2.6 34.7 + - - +
621B SER* 3.8 4.0 - - - -
623B ALA* 1.3 71.1 - - - +
625B THR* 1.3 66.1 + - - +
627B TYR* 4.4 4.0 - - - -
628B ASP* 3.0 49.0 + - - +
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Residues in contact with THR 625 (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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585B LEU* 4.6 27.1 - - + -
621B SER* 2.9 25.7 + - - -
622B LEU* 3.6 7.6 - - + -
624B THR* 1.3 78.8 - - - +
626B LEU* 1.3 62.6 + - + +
628B ASP* 3.7 4.7 + - - +
629B LYS* 3.3 23.0 + - + +
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Residues in contact with LEU 626 (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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550B MET* 5.0 1.6 - - - -
567B LEU* 3.5 32.1 - - + -
585B LEU* 4.7 7.9 - - + -
595B MET* 3.9 11.2 - - + -
598B LEU* 3.6 30.1 - - + -
622B LEU* 2.8 44.2 + - + +
623B ALA* 4.0 2.5 - - - +
625B THR* 1.3 70.4 - - - +
627B TYR* 1.3 68.1 + - - +
629B LYS* 2.9 15.2 + - - +
631B LEU* 3.2 32.8 + - + -
632B LEU* 3.9 23.6 - - + -
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Residues in contact with TYR 627 (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 LEU 3.7 20.7 + - - -
522B SER 3.5 9.0 + - - -
523B VAL* 3.4 34.5 + - + +
526B LEU* 3.3 38.8 - - + +
540B ALA* 6.1 0.2 - - + -
542B LEU* 4.0 20.0 - - + -
623B ALA 2.9 20.2 + - - +
624B THR 3.8 2.7 - - - +
626B LEU* 1.3 76.2 - - - +
628B ASP* 1.3 72.6 - - - +
630B GLY* 2.9 19.9 + - - -
632B LEU* 3.7 27.4 - - + +
633B LEU 5.0 0.2 - - - -
634B THR* 4.1 18.7 + - + -
638B LEU* 3.5 24.5 + - + +
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Residues in contact with ASP 628 (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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523B VAL* 4.3 17.6 - - + +
542B LEU* 5.1 1.6 - - - +
624B THR* 3.0 36.9 + - - +
625B THR* 4.1 5.1 - - - +
627B TYR* 1.3 96.2 - - - +
629B LYS* 1.3 61.4 + - - +
630B GLY 3.3 0.4 - - - -
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Residues in contact with LYS 629 (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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523B VAL* 4.6 0.7 - - - -
524B TYR* 3.8 7.1 + - - -
569B TYR* 3.1 32.5 - - + +
571B VAL* 3.8 10.5 - - + +
572B GLU* 2.9 30.5 + - + +
585B LEU* 4.3 14.6 - - + -
625B THR* 3.3 14.3 + - + +
626B LEU 2.9 10.9 + - - +
628B ASP* 1.3 80.1 + - - +
630B GLY* 1.3 63.4 + - - +
631B LEU* 3.3 13.9 + - + +
903B SO4 4.6 4.2 + - - -
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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