Contacts of the helix formed by residues 659 - 671 (chain D) in PDB entry 3H52
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 659 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610D TRP* 3.5 5.8 - - - -
614D ARG* 5.5 2.2 - - - +
658D VAL* 1.3 77.2 - - - +
660D TYR* 1.3 54.0 + - - +
661D GLU* 3.8 5.8 + - - +
662D GLU* 3.3 31.2 + - - +
663D TYR* 2.5 36.9 + - - +
700D ALA 5.0 1.0 + - - -
704D ARG* 4.3 18.4 - - - +
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Residues in contact with TYR 660 (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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537A GLU* 3.8 27.6 + - + -
540A GLU* 3.6 25.4 - - + +
610D TRP* 3.5 35.9 - + + -
614D ARG* 5.8 1.5 - - - +
659D SER* 1.3 71.0 - - - +
661D GLU* 1.3 61.5 + - + +
663D TYR* 3.6 11.6 - + - +
664D LEU* 2.8 67.9 + - + +
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Residues in contact with GLU 661 (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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531A THR* 5.7 2.5 - - - +
533A VAL* 3.5 41.1 - - + +
537A GLU* 5.3 10.5 - - - +
659D SER* 3.4 6.2 + - - +
660D TYR* 1.3 77.4 - - + +
662D GLU* 1.3 61.1 - - - +
664D LEU* 3.5 2.4 + - + +
665D CYS* 3.2 28.6 + - - -
699D LYS 5.6 0.2 - - - -
700D ALA* 4.0 17.2 - - + +
703D LYS* 3.8 37.0 - - + +
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Residues in contact with GLU 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D VAL* 3.5 10.1 - - + +
659D SER* 3.3 28.8 + - - +
660D TYR 3.3 0.4 - - - -
661D GLU* 1.3 74.4 - - - +
663D TYR* 1.3 65.5 + - - +
665D CYS* 3.2 3.3 + - - +
666D MET* 3.0 27.4 + - - +
697D LEU* 3.7 10.7 - - + +
700D ALA* 3.7 27.1 - - + +
701D ILE* 3.3 23.2 - - - +
704D ARG* 3.8 9.7 - - - -
714D ARG* 2.8 43.6 + - - -
718D LEU* 3.5 7.2 - - + +
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Residues in contact with TYR 663 (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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540A GLU* 4.3 4.7 + - - -
606D PHE* 3.6 35.2 - + - -
607D ALA* 3.2 23.4 - - - +
610D TRP* 3.0 69.7 - + + -
611D ARG* 5.9 0.3 - - - +
653D LEU* 5.0 1.3 - - + -
658D VAL* 3.6 7.3 - - + +
659D SER 2.5 22.0 + - - +
660D TYR* 3.6 19.5 - + - +
662D GLU* 1.3 73.1 - - - +
664D LEU* 1.3 64.7 + - + +
666D MET* 3.2 8.1 + - - +
667D LYS* 3.0 59.5 + - - +
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Residues in contact with LEU 664 (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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533A VAL* 4.4 10.3 - - + -
536A LEU* 3.8 23.7 - - + +
537A GLU* 3.8 24.2 - - + +
540A GLU* 3.4 40.4 - - + +
577D TRP* 5.5 0.3 - - - -
660D TYR* 2.8 65.0 + - + +
661D GLU* 3.9 4.5 - - + +
663D TYR* 1.3 76.2 - - + +
665D CYS* 1.3 62.2 + - - +
667D LYS* 3.8 4.4 + - - +
668D THR* 3.0 26.3 + - - -
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Residues in contact with CYS 665 (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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533A VAL* 4.0 9.9 - - - -
536A LEU* 4.4 8.5 - - - -
661D GLU 3.2 19.8 + - - -
662D GLU 3.6 6.7 - - - +
663D TYR 3.2 0.2 - - - -
664D LEU* 1.3 76.1 - - - +
666D MET* 1.3 65.5 - - - +
668D THR* 3.1 5.8 + - - -
669D LEU* 3.0 25.0 + - - +
693D TYR* 4.6 6.2 - - - +
696D GLU* 3.7 26.9 - - - -
697D LEU* 3.6 39.5 - - + +
700D ALA* 4.2 4.0 - - - -
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Residues in contact with MET 666 (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 PHE* 3.4 27.6 - - + -
653D LEU* 4.4 1.3 - - + -
658D VAL* 4.0 13.7 - - - -
662D GLU 3.0 19.2 + - - +
663D TYR* 3.5 6.7 - - - +
665D CYS* 1.3 76.5 - - - +
667D LYS* 1.3 56.6 + - - +
669D LEU* 3.1 8.2 + - - +
670D LEU* 2.9 23.0 + - - +
697D LEU* 3.8 19.7 - - + -
718D LEU* 3.6 42.8 - - + +
721D LEU* 3.8 26.0 - - + -
722D LEU* 3.3 30.0 - - + +
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Residues in contact with LYS 667 (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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540A GLU* 2.8 43.1 + - - -
541A PRO* 5.1 0.8 - - - +
577D TRP* 3.6 27.4 - - + -
603D LEU* 3.3 48.5 - - + +
606D PHE* 3.8 18.6 - - + -
607D ALA* 4.4 3.6 - - + -
663D TYR* 3.0 44.6 + - + +
664D LEU* 4.1 6.3 - - - +
666D MET* 1.3 77.3 - - - +
668D THR* 1.3 62.4 + - - +
670D LEU* 3.3 11.0 + - + +
671D LEU 3.3 0.9 + - - -
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Residues in contact with THR 668 (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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536A LEU* 3.4 15.9 - - - +
577D TRP* 3.8 10.2 - - + -
581D ILE* 3.7 27.2 - - + +
664D LEU 3.0 14.8 + - - -
665D CYS 3.1 8.1 + - - -
667D LYS* 1.3 75.5 - - - +
669D LEU* 1.3 63.7 + - - +
671D LEU* 3.3 12.2 + - + +
672D LEU* 3.4 17.6 - - + +
693D TYR* 3.7 44.4 - - + -
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Residues in contact with LEU 669 (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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665D CYS 3.0 14.3 + - - +
666D MET 3.1 8.0 + - - +
668D THR* 1.3 76.0 - - - +
670D LEU* 1.3 64.9 + - - +
672D LEU* 2.9 16.7 + - + +
673D SER* 3.1 11.6 + - - -
690D ARG* 3.9 25.6 + - + +
693D TYR* 4.1 12.3 - - + +
694D ILE* 3.6 41.7 - - + +
697D LEU* 3.8 30.1 - - + -
722D LEU* 3.8 18.4 - - + -
774D PHE* 4.1 15.0 - - + -
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Residues in contact with LEU 670 (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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599D SER* 3.7 10.4 - - - -
602D SER* 3.4 30.8 + - - +
603D LEU* 4.3 7.9 - - + -
606D PHE* 3.3 52.5 - - + -
666D MET 2.9 15.5 + - - +
667D LYS* 3.4 9.4 - - - +
668D THR 3.3 0.2 - - - -
669D LEU* 1.3 77.2 - - - +
671D LEU* 1.3 56.8 + - - +
673D SER* 2.9 36.4 + - - -
722D LEU* 3.8 21.5 - - + +
725D MET* 3.8 21.3 - - + -
726D HIS* 6.4 0.2 - - + -
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Residues in contact with LEU 671 (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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577D TRP* 3.7 24.0 - - + -
578D ALA* 3.8 20.4 - - + -
581D ILE* 4.4 10.1 - - + -
584D PHE* 3.8 32.8 - - + -
595D LEU* 4.0 17.9 - - - +
596D LEU* 4.1 15.3 - - + -
599D SER* 3.2 26.4 + - - +
603D LEU* 4.0 13.8 - - + +
667D LYS 3.3 3.9 + - - +
668D THR* 3.3 12.2 + - + +
669D LEU 3.2 0.4 - - - -
670D LEU* 1.3 78.6 - - - +
672D LEU* 1.3 62.8 + - + +
673D SER 3.4 0.8 + - - -
674D SER 5.3 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