Contacts of the helix formed by residues 610 - 617 (chain D) in PDB entry 5JA4
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 HIS 610 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B ALA* 5.1 1.2 - - - +
17B ARG* 4.5 7.7 + - - -
570D CYS 3.0 19.0 + - - +
571D ASN 2.9 27.1 - - - -
572D TYR* 3.3 6.7 + - - -
573D GLY 3.2 24.9 + - - +
605D ALA* 3.1 9.8 + - - +
606D LEU* 6.2 0.2 - - - -
608D CYS* 3.1 31.5 + - + +
609D GLY* 1.3 75.5 - - - +
611D PHE* 1.3 53.7 + - - +
612D GLU* 3.5 3.1 - - - -
613D VAL* 3.6 20.8 - - + +
614D ALA* 2.7 33.8 + - - +
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Residues in contact with PHE 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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606D LEU* 4.7 6.3 - - + -
609D GLY* 3.4 28.1 + - - -
610D HIS* 1.3 70.9 - - - +
612D GLU* 1.3 62.4 + - - +
613D VAL 3.1 1.3 - - - -
614D ALA* 3.4 6.0 - - + +
615D GLU* 2.6 38.3 + - - +
638D LEU* 3.8 17.7 - - + -
641D TRP* 3.6 35.7 - + - -
653D THR* 4.4 12.1 - - + -
656D LYS* 3.9 43.3 - - + +
657D ALA* 3.7 28.9 - - + -
660D MET* 4.1 25.2 - - + +
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Residues in contact with GLU 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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575D LEU* 4.0 25.1 - - + +
610D HIS* 5.2 0.7 - - - -
611D PHE* 1.3 81.7 + - - +
613D VAL* 1.3 58.3 + - + +
615D GLU* 3.5 7.5 + - - +
616D LEU* 3.1 25.6 + - - +
656D LYS* 2.9 39.1 + - - +
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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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570D CYS* 4.0 23.3 - - + +
573D GLY* 4.1 15.9 - - - -
575D LEU* 3.7 35.2 - - + +
578D VAL* 4.1 14.8 - - + -
605D ALA* 4.1 6.7 - - + -
610D HIS* 3.4 17.7 + - + +
611D PHE 3.1 0.4 - - - -
612D GLU* 1.3 74.2 - - + +
614D ALA* 1.3 65.2 + - - +
615D GLU 3.1 1.8 - - - -
616D LEU* 3.1 8.6 + - - +
617D LEU* 3.0 39.4 + - + +
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Residues in contact with ALA 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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602D LEU* 3.7 14.5 - - + +
605D ALA* 4.3 5.4 - - + -
606D LEU* 3.7 30.1 - - + -
610D HIS 2.7 21.4 + - - +
611D PHE* 3.1 8.3 + - - +
613D VAL* 1.3 73.2 - - - +
615D GLU* 1.3 60.9 + - - +
617D LEU* 3.5 6.3 + - - -
618D LEU* 3.2 25.8 + - - +
660D MET* 3.9 12.3 - - + -
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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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611D PHE 2.6 20.7 + - - +
612D GLU* 3.6 9.2 - - - +
613D VAL 3.1 0.2 - - - -
614D ALA* 1.3 69.8 - - - +
616D LEU* 1.3 65.5 + - - +
618D LEU* 3.2 38.3 + - - +
619D GLU* 3.6 19.5 + - - +
659D ALA* 5.5 6.8 - - - +
660D MET* 3.9 13.9 + - - +
663D LEU* 3.6 17.8 - - - +
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Residues in contact with LEU 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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575D LEU* 3.5 31.0 - - + +
578D VAL* 3.6 20.2 - - + +
579D ARG* 3.9 40.0 + - + +
582D LEU* 3.5 37.4 - - + +
612D GLU 3.1 12.1 + - - +
613D VAL 3.1 9.6 + - - +
615D GLU* 1.3 77.2 - - - +
617D LEU* 1.3 50.2 + - - +
618D LEU 3.1 0.7 + - - -
619D GLU* 2.8 42.2 + - - +
620D ARG* 4.8 2.0 - - + +
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Residues in contact with LEU 617 (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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566D LEU* 4.3 0.9 - - + -
570D CYS* 3.4 26.5 - - - -
582D LEU* 4.1 14.6 - - + -
588D VAL* 4.0 28.6 - - + +
601D PRO* 3.6 29.2 - - + +
602D LEU* 4.3 16.8 - - + +
605D ALA* 3.9 15.0 - - + -
613D VAL* 3.0 32.7 + - + +
614D ALA* 3.8 7.4 - - - +
615D GLU 3.3 0.4 - - - -
616D LEU* 1.3 76.4 - - - +
618D LEU* 1.3 51.0 + - - +
619D GLU 3.2 4.5 - - - +
621D GLY 2.5 28.1 + - - +
622D ALA* 4.0 4.0 - - - -
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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