Contacts of the helix formed by residues 701 - 719 (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 GLY 701 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697T ALA 3.5 4.8 + - - -
698T ILE 3.4 11.2 + - - -
699T DDE 3.7 1.4 - - - -
700T ARG* 1.3 81.3 - - - +
702T GLY* 1.3 56.0 + - - -
703T GLY 3.0 3.1 - - - -
704T GLN* 2.5 30.0 + - - -
705T ILE 3.0 8.5 + - - -
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Residues in contact with GLY 702 (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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662T SER* 3.2 27.6 + - - -
701T GLY* 1.3 69.0 - - - -
703T GLY* 1.3 57.1 + - - +
704T GLN 2.8 6.8 + - - -
706T ILE* 2.8 43.5 + - - +
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Residues in contact with GLY 703 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580T PRO* 4.4 5.0 - - - +
701T GLY 2.9 2.2 + - - -
702T GLY* 1.3 75.0 - - - +
704T GLN* 1.3 66.4 + - - +
706T ILE* 5.4 0.7 - - - -
707T PRO* 3.5 17.7 - - - +
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Residues in contact with GLN 704 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579T SER* 3.1 8.6 - - - -
580T PRO* 3.2 25.7 - - - +
581T ASN* 2.6 52.3 + - - +
584T ASN* 4.1 8.7 - - - +
698T ILE 5.1 0.2 - - - +
699T DDE 2.3 30.3 - - - +
700T ARG 4.2 1.3 - - - +
701T GLY* 2.5 18.3 + - - +
703T GLY* 1.3 78.6 + - - +
705T ILE* 1.3 54.3 + - - +
706T ILE 3.5 0.4 - - - -
707T PRO* 3.4 7.6 - - - +
708T THR* 2.6 26.3 + - - -
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Residues in contact with ILE 705 (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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584T ASN* 4.6 10.1 - - + -
586T ILE* 4.5 10.8 - - + -
659T ILE* 3.1 33.2 - - + -
662T SER* 3.7 22.2 - - - -
663T VAL* 4.2 20.6 - - + +
693T LEU* 3.8 17.7 - - + -
700T ARG* 2.8 35.7 - - - +
701T GLY 3.0 3.2 + - - +
704T GLN* 1.3 77.5 - - + +
706T ILE* 1.3 58.7 + - - +
707T PRO 3.3 0.4 - - - -
708T THR* 3.4 5.5 - - - +
709T MET* 2.9 27.9 + - - +
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Residues in contact with ILE 706 (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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662T SER* 3.5 28.5 - - - +
665T ALA* 4.2 16.8 - - + -
666T ALA* 3.2 21.7 - - + +
669T TRP* 3.9 31.4 - - + -
702T GLY* 2.8 35.1 + - - +
703T GLY* 5.4 0.2 - - - -
705T ILE* 1.3 70.6 - - - +
707T PRO* 1.3 64.3 - - + +
710T ARG* 3.1 20.3 + - - +
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Residues in contact with PRO 707 (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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578T LYS 5.6 0.2 - - - -
580T PRO* 4.3 17.3 - - + -
669T TRP* 5.8 5.4 - - + -
702T GLY 3.3 9.2 - - - +
703T GLY* 3.5 15.9 - - - +
704T GLN 3.4 13.0 - - - +
706T ILE* 1.3 98.5 - - + +
708T THR* 1.3 52.1 + - - +
710T ARG* 3.4 6.0 + - + +
711T ARG* 2.8 39.0 + - - +
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Residues in contact with THR 708 (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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577T SER* 3.6 26.2 - - - +
578T LYS* 3.8 16.2 - - - -
579T SER* 2.9 18.6 - - - +
584T ASN* 4.2 6.6 - - + +
585T ARG* 4.5 0.4 - - - -
586T ILE* 3.8 23.3 - - + +
704T GLN 2.6 23.0 + - - -
705T ILE* 3.3 11.7 + - - -
707T PRO* 1.3 78.3 - - - +
709T MET* 1.3 52.9 + - - +
711T ARG* 3.3 3.3 + - - +
712T ALA* 2.8 36.7 + - - +
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Residues in contact with MET 709 (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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586T ILE* 3.7 20.1 - - + +
588T LEU* 4.0 20.2 - - + -
646T VAL* 4.3 22.9 - - + -
663T VAL* 3.5 41.5 - - + +
666T ALA* 3.3 25.4 - - + -
667T PHE* 4.4 6.1 - - + +
686T VAL* 4.4 6.1 - - + -
688T ILE* 4.7 3.8 - - + -
705T ILE 2.9 13.2 + - - +
708T THR* 1.3 77.1 - - - +
710T ARG* 1.3 57.7 + - - +
712T ALA* 3.4 1.2 + - - +
713T THR* 2.9 54.4 + - - +
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Residues in contact with ARG 710 (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* 3.7 14.3 - - + +
669T TRP* 2.8 67.0 + - - +
670T ALA* 4.5 4.9 - - + +
673T GLU* 3.0 18.0 + - - -
706T ILE 3.1 17.9 + - - +
707T PRO* 3.8 6.1 - - + +
709T MET* 1.3 73.9 - - - +
711T ARG* 1.3 66.9 + - - +
713T THR* 3.8 5.1 - - - -
714T TYR* 2.5 75.7 + - + -
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Residues in contact with ARG 711 (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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577T SER* 3.6 3.6 - - - +
578T LYS 4.4 9.4 + - - -
707T PRO 2.8 20.2 + - - +
708T THR* 3.7 3.6 - - - +
710T ARG* 1.3 77.1 - - - +
712T ALA* 1.3 64.5 + - - +
714T TYR* 3.5 1.8 + - - +
715T ALA* 3.1 17.3 + - - +
836T GLN 5.0 0.2 + - - -
837T GLU 2.8 30.4 + - - -
838T TYR* 3.4 48.1 + - + +
839T TYR 4.0 3.4 + - - +
840T ASP* 2.7 41.3 + - - -
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Residues in contact with ALA 712 (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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575T ALA* 3.8 3.6 - - - +
577T SER* 3.2 21.2 + - - +
586T ILE* 4.1 19.7 - - + +
588T LEU* 3.6 28.9 - - + +
708T THR 2.8 18.3 + - - +
709T MET 3.8 1.6 - - - +
711T ARG* 1.3 77.9 - - - +
713T THR* 1.3 57.2 + - - +
715T ALA* 3.1 4.5 + - - +
716T GLY 2.8 26.3 + - - -
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Residues in contact with THR 713 (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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588T LEU* 4.0 10.7 - - - +
667T PHE* 4.4 9.8 - - + -
670T ALA* 3.7 24.7 - - + +
681T MET* 4.2 16.8 - - + -
684T VAL* 5.9 0.4 - - + -
686T VAL* 4.3 19.5 - - + +
709T MET* 2.9 46.2 + - - +
710T ARG 3.8 3.8 - - - -
711T ARG 3.3 0.2 - - - -
712T ALA* 1.3 76.5 - - - +
714T TYR* 1.3 57.9 + - - +
716T GLY* 3.2 0.9 + - - -
717T PHE* 2.8 30.2 + - + +
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Residues in contact with TYR 714 (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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670T ALA* 3.7 23.7 - - + -
673T GLU* 2.6 31.4 + - - +
674T GLY 4.8 0.2 - - - -
675T PRO* 3.6 33.2 - - + -
681T MET* 4.4 4.9 - - + -
710T ARG* 2.5 74.9 + - + +
711T ARG* 3.8 5.2 - - - +
713T THR* 1.3 75.3 - - - +
715T ALA* 1.3 57.2 - - - +
717T PHE* 3.3 5.0 + - - +
718T LEU* 2.9 35.8 + - - +
838T TYR* 3.7 34.5 - + + -
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Residues in contact with ALA 715 (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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575T ALA* 4.0 13.2 - - + -
577T SER* 4.3 1.3 - - - +
711T ARG 3.1 13.8 + - - +
712T ALA* 3.1 11.1 + - - +
714T TYR* 1.3 74.1 - - - +
716T GLY* 1.3 64.6 + - - +
718T LEU* 3.5 4.3 + - - +
719T LEU* 3.0 30.1 + - + +
835T TRP* 4.1 9.3 - - + +
838T TYR* 3.6 28.7 - - + +
839T TYR* 4.4 6.7 - - + +
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Residues in contact with GLY 716 (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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571T SER* 3.0 24.1 + - - -
575T ALA* 3.5 18.3 - - - +
588T LEU* 4.0 10.1 - - - -
590T ALA* 3.6 7.8 - - - +
712T ALA 2.8 16.4 + - - -
713T THR 3.7 1.8 - - - -
715T ALA* 1.3 72.1 - - - +
717T PHE* 1.3 64.5 + - - +
719T LEU* 3.3 3.1 + - - -
720T ALA* 3.2 13.2 + - - +
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Residues in contact with PHE 717 (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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565T GLU* 3.7 25.1 - - + -
566T THR* 3.3 32.3 - - - -
567T VAL* 3.4 30.0 - - + +
590T ALA* 4.0 5.5 - - + +
675T PRO* 3.5 17.5 - - + -
676T ILE* 3.8 17.5 - - + -
681T MET* 3.3 29.4 - - + -
684T VAL* 3.9 9.6 - - + -
713T THR* 2.8 17.1 + - + +
714T TYR* 3.4 5.4 - - - +
715T ALA 3.1 0.2 - - - -
716T GLY* 1.3 75.4 - - - +
718T LEU* 1.3 63.7 + - + +
720T ALA* 2.8 24.3 + - - +
722T PRO* 3.6 24.6 - - + +
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Residues in contact with LEU 718 (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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675T PRO* 3.9 18.6 - - + +
676T ILE* 4.7 7.0 - - + -
714T TYR 2.9 22.9 + - - +
717T PHE* 1.3 89.9 - - + +
719T LEU* 1.3 57.5 + - - +
720T ALA 3.1 0.4 - - - -
721T ASP 4.0 0.5 + - - -
722T PRO* 3.3 38.4 - - + +
809T LEU* 5.0 14.2 - - + +
832T VAL* 5.4 1.1 - - + -
833T PRO 3.9 13.9 - - - +
834T GLY* 4.4 1.1 - - - -
835T TRP* 3.5 33.6 - - + +
838T TYR* 3.7 30.7 - - + -
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Residues in contact with LEU 719 (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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570T GLU 3.9 0.3 - - - +
571T SER* 3.7 8.3 - - - -
572T SER* 2.7 53.8 + - - +
573T GLN* 3.3 37.9 - - + +
574T THR 4.3 0.7 - - - +
575T ALA* 4.2 17.7 - - + -
715T ALA 3.0 21.7 + - - +
716T GLY 3.7 5.2 - - - +
717T PHE 3.1 0.2 - - - -
718T LEU* 1.3 76.0 - - - +
720T ALA* 1.3 55.9 + - - +
721T ASP 3.5 2.8 + - - -
835T TRP* 3.4 51.1 - - + +
839T TYR* 4.7 2.7 - - + -
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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