Contacts of the helix formed by residues 655 - 673 (chain T) in PDB entry 2P8Z
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 TYR 655 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653T VAL* 3.6 2.8 - - - +
654T GLN* 1.3 107.4 + - + +
656T LEU* 1.3 63.7 + - - +
657T HIS* 3.5 10.5 - + - -
658T GLU* 3.4 36.0 + - - +
659T ILE* 3.6 6.4 - - - +
693T LEU* 3.4 29.6 - - + +
694T HIS 4.3 4.9 - - - -
695T ALA* 3.7 33.2 + - - +
700T ARG* 3.5 19.3 - - - +
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Residues in contact with LEU 656 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634T TRP* 3.6 29.6 - - + -
648T ASP* 3.7 17.9 - - - +
650T THR* 3.4 28.9 - - + +
653T VAL* 3.6 31.0 + - + +
654T GLN 3.3 4.6 + - - -
655T TYR* 1.3 73.9 - - - +
657T HIS* 1.3 67.9 + - - +
658T GLU 2.9 1.9 + - - -
659T ILE* 2.9 36.1 + - + +
660T LYS* 3.3 5.7 + - - -
688T ILE* 5.9 0.7 - - + -
691T VAL* 4.6 9.4 - - + -
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Residues in contact with HIS 657 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634T TRP* 5.9 0.7 - - - -
654T GLN 3.7 22.1 + - - -
655T TYR* 4.0 8.1 - + - -
656T LEU* 1.3 80.5 + - - +
658T GLU* 1.3 91.4 + - + +
659T ILE 3.6 0.5 + - - -
660T LYS* 3.7 20.3 + - - +
661T ASP* 5.0 1.0 + - - -
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Residues in contact with GLU 658 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655T TYR* 3.4 24.2 - - + +
656T LEU 2.9 1.6 + - - -
657T HIS* 1.3 106.8 + - + +
659T ILE* 1.3 62.3 + - + +
660T LYS 3.5 0.2 - - - -
661T ASP* 4.9 4.1 + - - +
662T SER* 5.1 2.8 + - - -
697T ALA* 5.4 2.8 - - - +
700T ARG* 2.5 36.1 + - - +
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Residues in contact with ILE 659 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586T ILE* 5.6 1.1 - - + -
634T TRP* 4.8 0.9 - - + -
655T TYR 3.6 11.4 - - - +
656T LEU* 2.9 31.2 + - + +
658T GLU* 1.3 79.4 - - + +
660T LYS* 1.3 68.0 + - - +
661T ASP 3.3 2.9 - - - -
662T SER* 2.9 10.4 + - - -
663T VAL* 2.9 37.6 + - + +
691T VAL* 3.7 32.3 - - + -
693T LEU* 3.7 15.7 - - + -
700T ARG* 4.5 6.5 - - + +
705T ILE* 3.1 36.6 - - + -
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Residues in contact with LYS 660 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633T ILE 5.7 0.6 + - - -
634T TRP* 3.8 75.2 + - + +
656T LEU 3.3 5.5 + - - +
657T HIS* 3.7 17.3 - - - +
658T GLU 3.5 0.8 - - - -
659T ILE* 1.3 76.5 - - - +
661T ASP* 1.3 69.2 + - - +
663T VAL* 3.2 2.3 + - - +
664T VAL* 2.9 34.3 + - + +
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Residues in contact with ASP 661 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657T HIS 5.0 0.6 + - - -
658T GLU 4.9 4.1 + - - +
659T ILE 3.3 1.0 - - - -
660T LYS* 1.3 83.1 - - - +
662T SER* 1.3 57.4 + - - +
664T VAL* 3.8 7.2 - - - +
665T ALA* 3.0 31.4 + - - +
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Residues in contact with SER 662 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658T GLU 5.1 2.3 + - - -
659T ILE* 2.9 14.7 + - - -
661T ASP* 1.3 78.9 - - - +
663T VAL* 1.3 58.3 + - - +
665T ALA* 3.4 1.1 + - - -
666T ALA* 3.0 30.2 + - - +
700T ARG 4.9 1.2 + - - -
701T GLY 4.5 0.2 - - - -
702T GLY* 3.2 24.8 + - - -
705T ILE* 3.7 24.1 - - - +
706T ILE* 3.5 22.9 - - - +
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Residues in contact with VAL 663 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586T ILE* 4.7 9.0 - - + -
634T TRP* 3.9 18.8 - - + -
646T VAL* 4.6 4.5 - - + -
659T ILE* 2.9 36.8 + - + +
660T LYS 3.6 5.6 - - - +
662T SER* 1.3 75.8 - - - +
664T VAL* 1.3 62.8 + - + +
666T ALA 3.2 1.6 + - - -
667T PHE* 3.0 20.8 + - - +
688T ILE* 3.8 21.1 - - + -
705T ILE* 4.2 10.5 - - + -
709T MET* 3.5 37.9 - - + +
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Residues in contact with VAL 664 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634T TRP* 4.0 20.9 - - + +
635T CYS* 3.8 35.7 - - + -
660T LYS* 2.9 33.9 + - + +
661T ASP* 3.8 8.1 - - - +
663T VAL* 1.3 73.6 - - - +
665T ALA* 1.3 65.4 + - - +
667T PHE* 3.0 13.7 + - - +
668T GLN* 3.0 23.8 + - + +
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Residues in contact with ALA 665 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661T ASP 3.0 19.3 + - - +
662T SER 3.7 3.4 - - - +
664T VAL* 1.3 78.0 - - - +
666T ALA* 1.3 62.0 + - - +
668T GLN* 3.3 12.0 + - - +
669T TRP* 3.1 21.5 + - - +
706T ILE* 4.2 19.5 - - + -
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Residues in contact with ALA 666 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662T SER 3.0 13.9 + - - +
665T ALA* 1.3 76.0 - - - +
667T PHE* 1.3 59.7 + - - +
669T TRP* 3.2 6.1 + - - +
670T ALA* 2.7 30.1 + - - +
706T ILE* 3.2 36.3 - - - +
709T MET* 3.3 28.9 - - + -
710T ARG* 3.7 7.3 - - + +
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Residues in contact with PHE 667 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635T CYS* 3.7 14.6 - - - -
637T GLY* 4.1 9.2 - - - -
644T ASN* 3.8 11.4 - - + -
645T LEU* 3.4 40.4 - - - -
646T VAL* 3.2 30.1 - - + -
663T VAL 3.0 13.3 + - - +
664T VAL 3.0 9.2 + - - +
666T ALA* 1.3 75.2 - - - +
668T GLN* 1.3 61.0 + - - +
670T ALA* 4.2 2.2 - - - +
671T THR* 2.8 63.9 + - + +
684T VAL* 4.4 4.7 - - + -
686T VAL* 3.8 21.3 - - + -
709T MET* 4.4 4.2 - - + +
713T THR* 4.4 18.4 - - + -
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Residues in contact with GLN 668 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635T CYS* 3.9 15.2 - - - +
636T PHE 2.9 23.3 + - - +
637T GLY* 4.1 1.9 - - - -
638T PRO* 3.3 6.4 - - - +
639T ASP* 3.1 12.2 + - - +
640T GLY* 2.8 30.5 + - - +
664T VAL* 3.0 35.1 + - + +
665T ALA* 3.3 9.6 + - - +
667T PHE* 1.3 76.2 - - - +
669T TRP* 1.3 59.7 + - - +
671T THR* 3.7 3.7 + - - -
672T LYS* 3.1 28.9 + - - +
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Residues in contact with TRP 669 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665T ALA 3.1 11.1 + - - +
666T ALA 3.4 8.3 - - - +
667T PHE 3.0 0.4 - - - -
668T GLN* 1.3 78.4 - - - +
670T ALA* 1.3 63.9 + - - +
672T LYS* 3.4 4.8 + - + +
673T GLU* 3.1 29.3 + - + +
706T ILE* 3.9 28.3 - - + -
707T PRO* 5.8 5.8 - - + -
710T ARG* 2.8 52.8 + - + +
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Residues in contact with ALA 670 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666T ALA 2.7 19.7 + - - +
667T PHE* 3.1 6.7 + - + +
669T TRP* 1.3 73.6 - - - +
671T THR* 1.3 61.0 + - - +
673T GLU 3.2 21.3 - - - +
674T GLY* 3.6 4.2 + - - -
681T MET* 3.9 4.9 - - - +
710T ARG* 4.5 6.7 - - + +
713T THR* 3.7 33.9 - - + -
714T TYR* 3.7 25.0 - - + -
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Residues in contact with THR 671 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637T GLY* 3.3 3.5 - - - -
638T PRO* 3.1 36.8 - - - +
644T ASN* 3.8 15.0 - - + -
667T PHE* 2.8 63.7 + - + +
668T GLN 3.7 0.9 + - - -
670T ALA* 1.3 69.9 - - - +
672T LYS* 1.3 61.3 + - - +
680T GLU* 3.4 4.5 - - - +
681T MET* 2.8 44.5 + - - -
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Residues in contact with LYS 672 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524T GLU* 5.7 0.6 + - - -
638T PRO* 3.7 14.6 - - + -
639T ASP* 4.3 17.9 + - - +
668T GLN 3.1 22.1 + - - +
669T TRP* 3.8 6.3 - - + +
671T THR* 1.3 79.1 + - - +
673T GLU* 1.3 60.7 + - + +
674T GLY 4.0 0.4 - - - -
678T GLY 4.1 2.9 - - - +
679T GLU 4.0 0.9 - - - -
680T GLU* 2.9 50.2 + - + +
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Residues in contact with GLU 673 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669T TRP* 3.1 20.9 + - + +
670T ALA 3.2 5.2 - - - +
672T LYS* 1.3 80.0 - - + +
674T GLY* 1.3 64.2 + - - +
678T GLY* 3.9 24.2 - - - +
710T ARG* 3.0 31.5 + - - -
714T TYR* 2.6 28.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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