Contacts of the helix formed by residues 653 - 664 (chain N) in PDB entry 5D4C
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 PHE 653 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644N LEU* 4.3 14.1 - - + -
649N ALA* 2.9 29.5 + - + +
650N LEU 4.0 1.1 - - - -
652N LEU* 1.3 77.2 - - + +
654N LYS* 1.3 64.2 + - - +
655N PRO* 3.3 4.7 - - - -
656N PHE* 2.9 34.0 + + - +
657N LEU* 3.0 8.7 + - - -
691N LEU* 4.3 6.3 - - + -
694N VAL* 4.2 20.0 - - + -
695N ILE* 3.8 31.4 - - + -
698N LYS* 4.4 21.8 - - + -
699N VAL 5.0 3.1 - - - -
700N VAL* 3.9 30.3 - - + -
718N PRO* 5.0 4.0 - - + -
749N VAL* 3.8 27.4 - - + -
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Residues in contact with LYS 654 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009M SER* 4.0 9.6 - - - +
650N LEU* 3.2 23.7 + - - +
651N GLU* 3.2 44.6 + - - +
652N LEU 3.2 0.6 - - - -
653N PHE* 1.3 76.1 - - - +
655N PRO* 1.3 65.2 - - + +
657N LEU* 3.1 6.9 + - - +
658N LEU* 2.9 35.6 + - + +
674N ARG* 4.1 38.6 - - - +
677N LEU* 3.6 44.8 + - + +
678N GLU* 6.3 1.1 - - - +
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Residues in contact with PRO 655 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009M SER* 4.4 4.0 - - - -
1067M TYR* 3.7 17.0 - - + -
1070M ILE* 3.5 22.7 - - + -
1071M ILE* 3.7 24.3 - - + +
625N TYR* 3.5 38.4 - - + +
652N LEU 4.3 0.2 - - - +
653N PHE 3.4 4.9 - - - +
654N LYS* 1.3 93.7 - - + +
656N PHE* 1.3 63.8 + - + +
658N LEU* 3.1 9.0 + - + +
659N LYS* 3.0 23.4 + - - +
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Residues in contact with PHE 656 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070M ILE* 3.5 45.3 - - + +
1074M GLU 6.1 0.7 - - - -
625N TYR* 5.4 2.0 - + - -
652N LEU 5.4 0.7 - - - -
653N PHE* 2.9 35.5 + + - +
655N PRO* 1.3 76.9 - - + +
657N LEU* 1.3 57.5 + - - +
659N LYS* 3.4 7.0 + - - +
660N LYS* 2.9 29.5 + - - +
694N VAL* 3.5 22.2 - - + +
698N LYS* 3.1 32.1 - - - -
749N VAL* 5.2 4.0 - - + -
751N LEU* 4.1 28.0 - - + -
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Residues in contact with LEU 657 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650N LEU* 3.7 36.1 - - + +
653N PHE 3.0 12.0 + - - +
654N LYS* 3.1 10.3 + - - +
656N PHE* 1.3 75.5 - - - +
658N LEU* 1.3 58.6 + - - +
660N LYS* 3.8 0.3 - - - +
661N MET* 2.9 39.5 + - + +
677N LEU* 3.7 25.8 - - + -
687N VAL* 3.5 26.0 - - + +
690N ALA* 4.2 8.5 - - + -
691N LEU* 3.6 31.6 - - + +
694N VAL* 4.0 6.4 - - + +
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Residues in contact with LEU 658 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067M TYR* 3.6 23.8 - - - +
1071M ILE* 4.4 2.5 - - + -
654N LYS* 2.9 23.0 + - + +
655N PRO* 3.1 12.1 + - + +
657N LEU* 1.3 73.7 - - - +
659N LYS* 1.3 66.0 + - - +
661N MET* 3.0 25.6 + - + +
662N GLU* 2.9 21.9 + - - +
670N VAL* 3.9 28.4 - - + +
673N ALA* 3.6 8.1 - - + +
674N ARG* 3.5 48.0 - - + +
677N LEU* 4.0 8.3 - - + -
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Residues in contact with LYS 659 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070M ILE 3.9 7.9 - - - +
1071M ILE 3.4 26.6 + - - +
1072M LYS* 4.1 17.0 + - - +
1073M GLY* 4.1 15.5 - - - -
655N PRO 3.0 11.6 + - - +
656N PHE* 3.7 8.7 - - - +
658N LEU* 1.3 76.9 - - - +
660N LYS* 1.3 57.6 + - - +
662N GLU* 3.1 24.3 + - - +
663N GLU* 2.9 61.4 + - - +
670N VAL* 5.1 1.1 - - - +
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Residues in contact with LYS 660 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656N PHE 2.9 17.6 + - - +
657N LEU* 3.8 3.4 - - - +
659N LYS* 1.3 76.8 - - - +
661N MET* 1.3 62.2 + - - +
663N GLU* 3.1 30.6 + - + +
664N LYS* 3.1 31.1 + - + +
690N ALA* 3.7 31.0 - - + +
693N GLU* 4.3 34.9 + - - +
694N VAL* 3.6 19.1 - - + +
48O MET* 5.6 1.0 - - - +
58O PRO* 4.9 14.8 - - - +
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Residues in contact with MET 661 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657N LEU* 2.9 33.4 + - + +
658N LEU* 3.0 24.2 + - + +
660N LYS* 1.3 76.2 - - - +
662N GLU* 1.3 53.5 + - - +
664N LYS 2.8 23.7 - - - +
666N ILE* 3.7 33.7 + - + -
667N ALA* 3.2 18.5 + - + -
673N ALA* 3.7 19.5 - - + -
676N MET* 4.6 4.3 - - - +
677N LEU* 3.5 38.1 - - + -
687N VAL* 4.0 22.9 - - + -
690N ALA* 4.8 0.7 - - + -
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Residues in contact with GLU 662 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071M ILE 4.7 1.2 - - - +
658N LEU 2.9 11.3 + - - +
659N LYS* 3.1 31.1 + - + +
661N MET* 1.3 75.5 - - - +
663N GLU* 1.3 63.5 + - - +
664N LYS 3.2 6.2 - - - +
667N ALA* 3.9 8.6 - - - +
668N PRO 3.9 15.7 - - - +
669N ASN* 3.2 30.5 - - - +
670N VAL* 3.3 20.4 + - + +
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Residues in contact with GLU 663 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659N LYS* 2.9 50.5 + - - +
660N LYS* 3.1 46.6 + - + +
662N GLU* 1.3 77.6 - - - +
664N LYS* 1.3 59.6 + - + +
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Residues in contact with LYS 664 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660N LYS* 3.1 31.2 + - + +
661N MET 2.8 16.9 - - - +
662N GLU 3.3 8.9 - - - +
663N GLU* 1.3 81.8 - - + +
665N GLY* 1.3 59.3 + - - +
666N ILE* 3.1 23.7 + - + +
667N ALA 3.9 3.6 - - - +
686N GLU* 5.0 3.2 + - - +
689N ASP* 4.9 0.6 - - - +
690N ALA* 4.5 11.8 - - + +
693N GLU* 2.9 32.2 + - - +
50O THR* 5.0 3.2 - - - +
51O LEU* 4.5 16.2 - - - +
52O GLU* 5.9 3.1 - - - -
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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