Contacts of the helix formed by residues 604 - 618 (chain A) in PDB entry 2X7G
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 604 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A SER* 4.1 7.6 - - - +
603A TYR* 1.3 83.4 - - - +
605A ARG* 1.3 59.2 + - - +
606A ASP* 3.4 9.8 + - - +
607A GLU* 3.3 28.7 + - - +
608A ASP* 2.9 23.0 + - - +
634A PHE* 4.2 5.7 - - - -
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Residues in contact with ARG 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ARG* 3.6 30.6 - - - +
597A PRO* 3.5 37.8 + - + +
598A HIS* 3.7 12.1 - - - +
599A SER* 4.1 11.7 + - - +
604A SER* 1.3 72.4 - - - +
606A ASP* 1.3 60.5 + - - +
608A ASP 3.2 0.7 + - - -
609A HIS* 2.8 28.6 + - - +
1703A SO4 3.6 15.3 + - - -
1704A SO4 3.4 29.6 + - - -
1706A SO4 2.6 43.0 + - - -
1707A ACT 3.9 1.4 + - - -
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Residues in contact with ASP 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ARG* 2.9 34.6 + - - +
562A ARG* 4.6 1.4 + - - -
567A LEU* 3.5 19.4 - - + +
604A SER* 3.3 5.4 + - - +
605A ARG* 1.3 77.8 - - - +
607A GLU* 1.3 57.8 + - - +
609A HIS* 3.0 4.1 + - - +
610A ILE* 2.9 34.1 + - + +
630A TYR* 6.1 0.9 - - - -
634A PHE* 3.5 32.1 - - + -
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Residues in contact with GLU 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A TYR* 4.0 8.1 - - + -
604A SER* 3.3 28.9 + - - +
605A ARG 3.2 0.4 - - - -
606A ASP* 1.3 77.4 - - - +
608A ASP* 1.3 66.3 + - - +
610A ILE* 3.2 5.6 + - - +
611A ALA* 3.0 22.7 + - - +
633A GLU 4.7 1.3 - - - +
634A PHE* 3.6 40.8 - - + +
641A LEU* 4.7 10.8 - - + +
642A ARG 4.3 0.5 + - - -
643A HIS* 2.9 55.4 + - - +
644A ILE* 3.8 10.7 + - + +
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Residues in contact with ASP 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 3.2 9.9 - - - +
598A HIS* 3.0 46.3 + - - +
603A TYR* 3.9 17.6 + - + -
604A SER 2.9 9.2 + - - +
605A ARG 3.6 4.5 - - - +
607A GLU* 1.3 76.2 - - - +
609A HIS* 1.3 63.9 + - - +
611A ALA* 3.1 4.9 + - - +
612A HIS* 3.0 51.0 + - - -
644A ILE* 4.0 13.1 - - - +
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Residues in contact with HIS 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ARG* 3.2 54.0 + - - +
560A GLN 4.6 0.6 + - - -
562A ARG 3.8 20.2 + - - -
567A LEU* 3.7 14.2 - - + +
595A PHE* 3.6 36.0 - + + +
597A PRO* 3.8 15.5 - - + -
605A ARG 2.8 14.3 + - - +
606A ASP 3.0 8.5 + - - +
608A ASP* 1.3 75.8 - - - +
610A ILE* 1.3 62.6 + - - +
612A HIS* 3.2 6.7 + - + +
613A ILE* 3.1 33.1 + - + +
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Residues in contact with ILE 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A ILE* 4.1 14.1 - - + -
567A LEU* 4.2 11.9 - - + -
568A ILE* 4.2 13.5 - - + -
606A ASP 2.9 20.4 + - - +
607A GLU* 3.8 5.6 - - - +
609A HIS* 1.3 76.0 - - - +
611A ALA* 1.3 62.7 + - - +
613A ILE* 3.3 8.5 + - - +
614A ILE* 3.2 29.8 + - + +
620A ILE* 3.9 25.4 - - + -
634A PHE* 3.4 43.3 - - + -
635A PHE* 3.9 13.5 - - + -
641A LEU* 4.4 6.5 - - + -
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Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A GLU 3.0 12.1 + - - +
608A ASP* 3.1 12.5 + - - +
610A ILE* 1.3 77.4 - - - +
612A HIS* 1.3 58.5 + - + +
614A ILE* 3.3 4.3 + - - +
615A GLU* 3.0 35.6 + - - +
641A LEU* 4.6 8.9 - - + +
644A ILE* 3.8 20.9 - - + -
647A LEU* 3.9 22.2 - - + +
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Residues in contact with HIS 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A PHE* 3.9 20.4 - - + -
596A GLU 5.3 7.4 + - - +
597A PRO* 4.8 8.5 - - + +
598A HIS* 6.1 0.2 + - - -
608A ASP* 3.0 54.4 + - - -
609A HIS* 3.2 7.6 + - + +
611A ALA* 1.3 78.1 - - + +
613A ILE* 1.3 62.7 + - - +
615A GLU* 3.7 20.8 + - - +
616A LEU* 3.1 24.1 + - - +
1711A EDO 5.7 7.8 + - - -
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Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A ARG 5.1 0.2 - - - +
564A ILE* 3.9 18.2 - - + -
567A LEU* 3.7 29.8 - - + -
579A TRP* 3.8 28.0 - - + -
595A PHE* 3.8 25.1 - - + -
609A HIS* 3.1 23.6 + - + +
610A ILE* 3.6 8.3 - - - +
611A ALA 3.1 0.2 - - - -
612A HIS* 1.3 79.1 - - - +
614A ILE* 1.3 53.5 + - + +
616A LEU* 3.3 0.9 + - - +
617A LEU* 2.8 38.7 + - + +
620A ILE* 5.1 0.4 - - + -
680A MET* 3.8 26.7 - - - -
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Residues in contact with ILE 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ILE* 3.2 32.2 + - + +
611A ALA 3.6 4.0 - - - +
612A HIS 3.3 0.2 - - - -
613A ILE* 1.3 72.1 - - - +
615A GLU* 1.3 69.0 + - - +
618A GLY* 2.9 40.5 + - - +
619A SER* 4.3 7.0 - - - +
620A ILE* 3.8 29.4 - - + +
635A PHE* 4.9 4.7 - - + -
641A LEU* 4.1 23.1 - - + -
647A LEU* 3.8 22.0 - - + -
649A PRO* 5.8 0.2 - - - +
1713A EDO 4.6 0.9 - - - -
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Residues in contact with GLU 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ALA* 3.0 21.8 + - - +
612A HIS* 3.7 31.1 + - - +
613A ILE 3.3 0.2 - - - -
614A ILE* 1.3 79.7 - - - +
616A LEU* 1.3 57.7 + - - +
646A LYS 4.4 1.6 - - - +
647A LEU* 3.4 23.8 - - + +
648A LYS* 2.7 47.7 + - - +
649A PRO* 3.4 8.9 - - - +
650A TRP* 3.0 26.3 + - + +
1713A EDO 3.7 5.4 + - - -
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Residues in contact with LEU 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A LEU* 4.1 22.0 - - + -
595A PHE* 3.7 28.7 - - + -
612A HIS 3.1 16.1 + - - +
613A ILE 3.8 2.7 - - - +
614A ILE 3.1 0.4 - - - -
615A GLU* 1.3 78.4 - - - +
617A LEU* 1.3 76.6 + - + +
618A GLY 3.7 0.7 - - - -
650A TRP 3.6 17.0 - - - +
651A SER* 3.8 7.6 - - - -
652A LEU* 3.7 36.7 + - + +
655A VAL* 4.4 10.1 - - + -
678A LEU* 4.7 3.4 - - + -
1710A EDO 4.8 2.4 + - - -
1711A EDO 4.8 8.5 - - - -
1713A EDO 3.5 17.1 - - - -
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Residues in contact with LEU 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A TRP* 4.0 19.1 - - + -
595A PHE* 4.7 2.5 - - + -
613A ILE* 2.8 25.2 + - + +
616A LEU* 1.3 98.0 - - + +
618A GLY* 1.3 59.8 + - - +
619A SER 4.8 0.3 - - - +
652A LEU* 5.5 0.4 - - + -
675A ILE* 3.6 30.7 - - + -
678A LEU* 3.6 41.7 - - + +
680A MET* 4.4 17.7 - - + +
1710A EDO 5.5 1.8 + - - -
1713A EDO 4.1 10.4 + - - -
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Residues in contact with GLY 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ILE* 2.9 31.4 + - - +
616A LEU 3.7 0.8 - - - -
617A LEU* 1.3 78.4 - - - +
619A SER* 1.3 69.9 + - - +
620A ILE 3.5 0.9 + - - -
680A MET* 3.4 10.0 - - - +
1713A EDO 3.9 13.5 - - - -
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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
------------------------------------------------------------
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