Contacts of the helix formed by residues 670 - 687 (chain A) in PDB entry 4GT4
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 670 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A VAL* 3.7 15.7 - - - -
662A GLU* 5.1 3.1 + - - +
669A PHE* 1.3 75.2 - - - +
671A ILE* 1.3 61.7 + - - +
672A ASP* 3.6 18.7 + - - +
673A SER* 2.8 26.9 + - - -
674A ASP* 3.0 20.1 + - - -
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Residues in contact with ILE 671 (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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603A MET* 5.6 1.6 - - + -
607A SER* 3.9 27.8 - - - +
610A HIS* 5.3 2.9 - - - -
611A VAL 3.7 25.6 - - - +
612A VAL* 4.1 14.6 - - + +
670A SER* 1.3 74.7 - - - +
672A ASP* 1.3 61.3 + - - +
674A ASP* 3.1 13.3 + - + +
675A ILE* 2.9 27.1 + - + +
738A ARG* 3.9 15.3 - - - +
739A PHE* 4.1 8.5 - - + -
801A NO3 3.7 24.5 - - - +
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Residues in contact with ASP 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A GLU* 4.5 1.1 - - - +
670A SER* 3.4 9.8 + - - +
671A ILE* 1.3 75.5 - - - +
673A SER* 1.3 57.5 + - - +
675A ILE* 2.9 26.7 + - - +
676A TRP 3.0 10.4 + - - -
733A PRO* 3.4 37.7 - - + +
734A SER* 4.2 5.2 + - - -
736A ARG* 3.1 16.9 + - - +
738A ARG* 2.6 40.2 + - - -
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Residues in contact with SER 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A MET* 6.1 0.2 - - - -
660A ALA* 4.0 14.8 + - - +
662A GLU* 4.0 11.4 + - - -
663A ALA* 4.2 15.0 - - - -
668A LYS 4.8 0.9 - - - -
669A PHE* 3.6 10.5 - - - +
670A SER* 2.8 40.1 + - - -
672A ASP* 1.3 79.2 - - - +
674A ASP* 1.3 58.0 + - - +
676A TRP* 3.3 2.8 + - - +
677A SER* 2.9 33.7 + - - -
736A ARG* 3.5 9.5 - - - +
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Residues in contact with ASP 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A MET* 3.8 23.5 - - + +
612A VAL* 3.7 5.5 - - - +
613A HIS* 2.7 48.4 + - - +
614A LYS* 4.9 0.5 - - - -
616A LEU* 3.5 15.0 + - + +
669A PHE* 5.4 1.6 - - - +
670A SER 3.0 22.0 + - - +
671A ILE* 3.2 18.1 - - + +
672A ASP 3.1 0.4 - - - -
673A SER* 1.3 79.8 + - - +
675A ILE* 1.3 53.9 + - - +
677A SER* 3.5 6.4 + - - -
678A TYR* 2.9 26.9 + - - +
739A PHE* 3.5 4.4 - - + -
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Residues in contact with ILE 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ILE 2.9 17.6 + - - +
672A ASP* 2.9 10.4 + - - +
674A ASP* 1.3 74.5 - - - +
676A TRP* 1.3 66.3 + - - +
678A TYR* 3.0 4.4 + - - +
679A GLY 2.9 18.2 + - - -
728A CYS* 3.6 23.6 - - + +
736A ARG* 3.8 18.2 - - + +
737A PRO 3.2 28.3 - - - +
738A ARG* 3.6 41.1 - - - +
739A PHE* 3.6 22.7 - - + -
742A ILE* 4.3 4.3 - - + -
801A NO3 4.3 4.0 - - - +
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Residues in contact with TRP 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ARG 5.4 1.0 + - - -
658A TRP 3.6 15.7 - - - -
659A MET 3.4 15.6 + - - -
660A ALA* 3.7 14.6 - - + -
661A PRO* 3.5 31.6 - - + -
672A ASP 3.0 10.0 + - - +
673A SER 3.3 8.9 + - - +
675A ILE* 1.3 76.6 - - - +
677A SER* 1.3 59.6 - - - +
679A GLY 2.9 17.0 + - - -
680A VAL* 3.0 23.4 + - + +
693A TYR* 5.5 5.8 - - - -
705A ILE* 4.6 12.2 - - + +
708A ARG* 5.9 5.8 - - + -
710A VAL* 4.6 11.7 - - + -
728A CYS 3.5 12.2 + - - +
729A TRP* 3.3 62.6 + + + -
730A ASN 3.8 7.4 - - - -
731A GLU* 4.8 1.3 - - - -
736A ARG* 3.6 20.2 - - - +
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Residues in contact with SER 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LEU* 3.9 28.3 + - - +
658A TRP* 2.6 29.5 + - - +
659A MET* 4.5 2.8 - - - +
673A SER* 2.9 19.0 + - - -
674A ASP* 3.6 9.4 + - - -
675A ILE 3.3 0.2 - - - -
676A TRP* 1.3 76.0 - - - +
678A TYR* 1.3 57.9 + - - +
680A VAL* 3.3 6.7 + - - +
681A VAL* 2.9 31.4 + - - +
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Residues in contact with TYR 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A VAL* 2.6 27.1 + - - +
599A ILE* 3.7 31.9 - - + -
600A ALA* 3.4 17.1 - - + +
603A MET* 4.9 0.4 - - + -
616A LEU* 3.8 10.5 - - + +
674A ASP 2.9 15.2 + - - +
675A ILE 3.0 8.0 + - - +
677A SER* 1.3 76.2 - - - +
679A GLY* 1.3 61.4 + - - +
681A VAL* 3.0 10.5 + - + +
682A LEU* 2.9 50.8 + - + +
728A CYS* 4.2 4.7 - - - -
739A PHE* 3.6 20.2 - + + -
742A ILE* 3.7 33.4 - - + -
746A LEU* 3.2 18.2 - - - +
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Residues in contact with GLY 679 (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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675A ILE 2.9 7.7 + - - -
676A TRP 2.9 8.4 + - - -
678A TYR* 1.3 77.3 - - - +
680A VAL* 1.3 61.5 + - - +
682A LEU* 3.0 18.9 + - - +
683A TRP 2.9 17.8 + - - -
725A MET* 4.0 2.6 - - - +
728A CYS* 3.8 16.4 - - - -
729A TRP* 3.6 21.1 - - - -
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Residues in contact with VAL 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ARG 3.8 16.2 - - - +
658A TRP* 3.4 27.4 - - + +
676A TRP* 3.0 31.9 + - + +
677A SER 3.4 7.2 - - - +
678A TYR 3.2 0.2 - - - -
679A GLY* 1.3 75.2 - - - +
681A VAL* 1.3 57.1 + - - +
683A TRP* 3.3 3.8 + - - +
684A GLU* 2.9 26.4 + - - +
692A PRO* 3.6 25.4 - - + -
711A LEU* 4.0 8.5 - - + -
729A TRP* 3.4 20.6 - - + +
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Residues in contact with VAL 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A VAL* 5.4 1.6 - - + -
599A ILE* 3.9 34.8 - - + -
616A LEU* 3.9 18.2 - - + +
617A ALA* 3.7 31.0 - - - -
618A THR* 4.2 10.5 - - + +
621A VAL* 5.7 0.2 - - + -
658A TRP* 4.6 0.4 - - + -
677A SER 2.9 18.4 + - - +
678A TYR* 3.2 15.9 - - + +
680A VAL* 1.3 74.5 - - - +
682A LEU* 1.3 65.8 + - - +
684A GLU* 3.1 10.1 + - - +
685A VAL* 2.9 26.2 + - + +
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Residues in contact with LEU 682 (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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596A VAL* 3.6 40.2 - - + -
678A TYR* 2.9 39.5 + - + +
679A GLY* 3.2 14.1 - - - +
681A VAL* 1.3 75.5 - - - +
683A TRP* 1.3 64.4 + - - +
685A VAL* 3.3 0.5 + - - +
686A PHE* 2.9 30.1 + - + +
721A VAL* 4.4 10.3 - - + +
724A LEU* 3.9 34.8 - - + -
725A MET* 3.7 32.1 - - + +
728A CYS* 4.6 0.9 - - - -
746A LEU* 5.1 0.4 - - + -
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Residues in contact with TRP 683 (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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679A GLY 2.9 11.8 + - - +
680A VAL 3.3 9.0 - - - +
682A LEU* 1.3 77.2 - - - +
684A GLU* 1.3 59.0 + - - +
686A PHE 3.4 1.0 + - - -
687A SER* 2.7 55.2 + - - -
690A LEU* 3.2 38.4 - - + -
691A GLN 3.8 11.9 - - - -
692A PRO* 3.6 26.7 - - + -
693A TYR 4.6 2.5 - - - -
694A CYS* 5.4 1.8 - - + -
711A LEU* 3.7 33.4 - - + +
712A PRO* 2.7 43.3 + - + +
714A PRO* 3.6 17.8 - - + +
725A MET* 3.6 18.5 - - - +
729A TRP* 4.3 1.3 - + + -
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Residues in contact with GLU 684 (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 HIS* 4.0 12.0 - - - -
565A LEU* 4.6 0.2 - - - -
617A ALA* 3.6 1.6 - - - +
618A THR* 2.6 48.3 + - + +
619A ARG* 4.7 0.9 + - - +
658A TRP* 2.6 43.4 + - - +
680A VAL 2.9 14.8 + - - +
681A VAL* 3.3 12.4 - - - +
683A TRP* 1.3 80.2 - - - +
685A VAL* 1.3 61.1 + - - +
687A SER* 3.0 8.0 + - - -
689A GLY* 2.8 30.1 + - - +
690A LEU 4.1 17.0 - - - +
692A PRO* 4.3 8.7 - - + +
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Residues in contact with VAL 685 (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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561A LEU* 4.3 10.5 - - + -
565A LEU* 3.7 15.8 - - + +
592A PHE* 3.5 44.5 - - + +
595A LEU* 4.4 10.3 - - + -
596A VAL* 3.9 28.7 - - + -
599A ILE* 4.9 1.6 - - + -
618A THR* 4.0 16.6 - - + -
681A VAL* 2.9 25.5 + - + +
682A LEU 3.7 3.8 - - - +
684A GLU* 1.3 75.9 - - - +
686A PHE* 1.3 63.3 + - + +
688A TYR* 3.3 11.6 + - - -
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Residues in contact with PHE 686 (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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571A HIS* 6.0 0.5 - - - -
589A PRO 5.6 0.7 - - - -
592A PHE* 3.7 32.5 - + + -
593A VAL* 4.6 9.9 - - + -
596A VAL* 4.4 19.7 - - + -
682A LEU* 2.9 23.4 + - + +
683A TRP 3.6 2.7 - - - +
685A VAL* 1.3 80.1 - - + +
687A SER* 1.3 58.5 + - - +
688A TYR* 3.4 11.7 - - - -
714A PRO* 3.4 16.8 - - + +
715A ASP 4.3 8.3 - - - +
717A CYS* 4.0 18.8 - - + -
718A PRO* 3.7 32.1 - - + -
721A VAL* 3.7 32.3 - - + -
725A MET* 4.5 0.4 - - + -
802A NO3 3.7 27.7 + - - -
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Residues in contact with SER 687 (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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569A SER* 4.8 2.6 + - - -
571A HIS* 5.7 3.8 - - - -
683A TRP* 2.7 50.7 + - - -
684A GLU 3.0 2.6 + - - -
686A PHE* 1.3 77.2 - - - +
688A TYR* 1.3 73.1 - - - +
689A GLY 3.3 1.0 + - - -
690A LEU* 3.4 23.6 + - - +
714A PRO* 3.3 21.0 - - - +
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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