Contacts of the helix formed by residues 607 - 616 (chain D) in PDB entry 4CYM
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 ASN 607 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605D ALA* 3.5 5.4 - - - +
606D LEU* 1.3 95.0 - - - +
608D SER* 1.3 66.0 + - - +
609D LYS* 3.1 44.8 - - - +
610D ILE* 3.2 28.5 + - - +
611D LEU* 3.2 24.0 + - - +
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Residues in contact with SER 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607D ASN* 1.3 72.0 - - - +
609D LYS* 1.3 69.0 + - - +
610D ILE 3.1 0.4 - - - -
611D LEU* 3.6 10.9 - - - +
612D SER* 3.1 22.3 + - - -
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Residues in contact with LYS 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D GLN* 6.2 0.2 - - - +
607D ASN* 3.1 39.6 - - - +
608D SER* 1.3 78.5 + - - +
610D ILE* 1.3 62.5 + - + +
612D SER* 2.5 29.0 + - - -
613D VAL* 3.3 9.7 + - + +
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Residues in contact with ILE 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D ALA* 4.6 2.7 - - - +
576D GLY* 3.3 35.0 - - - +
578D GLN* 5.6 8.1 - - + +
581D ILE* 4.1 18.2 - - + -
605D ALA* 3.8 19.3 - - + -
606D LEU* 3.9 13.0 - - + +
607D ASN* 3.2 33.5 + - - +
608D SER 3.1 0.6 - - - -
609D LYS* 1.3 77.7 - - + +
611D LEU* 1.3 67.9 + - - +
612D SER 3.0 1.1 - - - -
613D VAL* 2.8 23.9 + - + +
614D MET* 3.0 25.5 + - + +
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Residues in contact with LEU 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D LEU* 3.8 38.6 - - + +
605D ALA* 4.0 7.1 - - + +
607D ASN 3.2 16.9 + - - +
608D SER* 3.6 12.3 - - - +
610D ILE* 1.3 77.7 - - - +
612D SER* 1.3 56.3 + - - +
614D MET* 3.3 7.0 + - + +
615D GLU* 2.8 63.2 + - - +
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Residues in contact with SER 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D SER 3.1 9.8 + - - -
609D LYS* 2.5 21.9 + - - -
610D ILE 3.0 0.8 - - - -
611D LEU* 1.3 78.0 - - - +
613D VAL* 1.3 67.3 + - - +
615D GLU* 3.1 12.8 + - - +
616D ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D GLN* 3.3 29.6 - - + +
581D ILE* 5.1 9.9 - - + -
582D GLU* 4.0 30.1 - - + +
585D LEU* 5.2 0.4 - - + -
609D LYS* 3.4 16.8 - - + +
610D ILE* 2.8 16.1 + - + +
612D SER* 1.3 82.7 + - - +
614D MET* 1.3 60.2 + - + +
616D ALA* 3.1 22.2 - - + +
617D TYR* 3.4 15.6 - - + -
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Residues in contact with MET 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D LEU* 4.2 19.1 - - + -
573D ALA* 4.0 17.0 - - + -
581D ILE* 4.0 20.0 - - + -
585D LEU* 4.3 9.7 - - + +
591D THR* 4.3 11.4 - - + +
601D PRO* 3.8 40.4 - - + +
602D LEU* 3.8 20.9 - - + +
605D ALA* 4.5 6.1 - - - -
610D ILE* 3.0 30.6 + - + +
611D LEU* 3.5 8.1 - - + +
613D VAL* 1.3 75.2 - - - +
615D GLU* 1.3 63.2 - - - +
617D TYR* 3.3 15.2 + - - +
618D HIS* 3.5 9.9 + - - +
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Residues in contact with GLU 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D LEU* 5.0 10.2 - - + +
611D LEU* 2.8 56.3 + - - +
612D SER* 3.6 7.8 - - - +
614D MET* 1.3 72.8 - - - +
616D ALA* 1.3 66.5 + - - +
618D HIS* 3.0 35.8 + - + -
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Residues in contact with ALA 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D SER 2.9 12.6 + - - +
613D VAL* 3.1 22.9 - - + +
615D GLU* 1.3 75.5 - - - +
617D TYR* 1.3 65.3 + - + +
618D HIS 4.8 0.9 - - - -
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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