Contacts of the helix formed by residues 611 - 626 (chain N) in PDB entry 5GJQ
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 ASN 611 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576N PRO* 2.5 45.7 - - + +
609N ASP* 2.7 24.2 + - - +
610N VAL* 1.3 73.8 - - - +
612N ASP* 1.3 79.8 + - - +
613N ASP* 2.8 25.1 + - - +
614N VAL* 3.6 6.4 - - - +
615N ARG* 3.3 16.8 + - - +
177U ARG* 6.1 0.7 - - - +
178U ASP* 5.2 2.1 + - - +
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Residues in contact with ASP 612 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J ARG* 5.5 1.9 + - - -
610N VAL 3.2 12.6 + - - +
611N ASN* 1.3 74.1 + - - +
613N ASP* 1.3 54.5 + - - +
614N VAL 3.1 2.0 - - - -
615N ARG* 2.8 24.0 + - - +
616N ARG* 2.4 35.3 + - - +
645N ASN* 3.0 26.1 + - - +
647N HIS* 3.2 39.2 + - + +
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Residues in contact with ASP 613 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580N ARG* 5.8 3.1 - - + -
611N ASN* 2.8 20.5 + - - +
612N ASP* 1.3 73.4 - - - +
614N VAL* 1.3 52.2 + - + +
616N ARG* 2.8 37.6 + - - +
617N ALA* 2.3 40.4 + - - +
647N HIS* 3.2 9.6 - - - -
770N TRP* 3.5 23.4 - - - -
771N PHE* 6.0 0.3 - - - -
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Residues in contact with VAL 614 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576N PRO* 3.4 42.0 - - + +
579N ARG* 4.1 12.1 - - + +
580N ARG* 4.1 24.7 - - + +
583N MET* 6.4 0.7 - - + -
605N VAL* 4.7 11.9 - - + -
609N ASP* 3.0 34.1 - - + +
611N ASN* 3.6 5.6 - - - +
613N ASP* 1.3 77.5 - - + +
615N ARG* 1.3 51.1 - - - +
617N ALA* 3.1 6.9 + - - +
618N ALA* 2.3 41.3 + - + +
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Residues in contact with ARG 615 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J ARG* 4.2 19.6 - - - +
64K GLU* 5.4 4.8 + - - -
67K ASN* 2.7 40.8 + - - +
606N ALA* 3.0 35.2 + - + +
607N VAL 4.2 2.7 + - - -
609N ASP* 2.2 34.0 + - + +
610N VAL* 3.9 7.1 + - - +
611N ASN 3.3 12.5 + - - +
612N ASP* 2.8 29.8 + - - +
614N VAL* 1.3 74.1 - - - +
616N ARG* 1.3 53.5 + - - +
618N ALA* 2.9 8.4 + - - -
619N VAL* 2.4 43.8 + - + +
645N ASN* 4.7 1.2 - - - +
648N VAL* 4.4 26.7 - - + +
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Residues in contact with ARG 616 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612N ASP 2.4 16.0 + - - +
613N ASP* 2.8 29.4 + - - +
615N ARG* 1.3 70.8 - - - +
617N ALA* 1.3 53.7 + - - +
619N VAL* 3.0 5.7 + - - +
620N GLU* 2.7 42.2 + - + +
646N PRO* 4.2 4.0 - - - +
647N HIS* 2.8 64.8 + - + +
648N VAL 5.0 0.2 - - - +
650N TYR* 2.0 61.3 - - + +
651N GLY* 3.5 12.9 - - - +
682N TYR* 5.0 6.7 - - - -
683N VAL* 5.6 0.8 - - - +
770N TRP* 3.2 17.4 - - - +
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Residues in contact with ALA 617 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580N ARG* 4.4 25.4 - - + +
583N MET* 4.7 1.1 - - + -
584N TYR* 5.6 6.1 - - + -
613N ASP 2.3 27.5 + - - +
614N VAL* 3.1 12.6 - - - +
616N ARG* 1.3 68.2 - - - +
618N ALA* 1.3 52.6 + - - +
620N GLU* 2.6 31.2 + - - +
621N SER* 2.7 21.6 + - - -
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Residues in contact with ALA 618 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583N MET* 3.8 20.3 - - + +
602N LEU* 4.0 14.4 - - - +
605N VAL* 4.8 8.5 - - + -
606N ALA* 3.6 25.1 - - + +
614N VAL* 2.3 33.0 + - + +
615N ARG* 3.3 5.4 - - - +
617N ALA* 1.3 67.8 - - - +
619N VAL* 1.3 61.3 + - - +
621N SER* 3.6 2.3 + - - -
622N LEU* 3.1 27.0 + - - +
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Residues in contact with VAL 619 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606N ALA* 4.4 11.0 - - + -
615N ARG* 2.4 30.6 + - + +
616N ARG* 3.2 8.5 - - - +
618N ALA* 1.3 69.2 - - - +
620N GLU* 1.3 68.3 + - - +
622N LEU* 3.1 27.4 - - + +
637N VAL* 5.1 5.6 - - + -
640N LEU* 3.6 32.1 - - + -
648N VAL* 4.6 13.0 - - + +
651N GLY* 3.3 26.2 - - - +
652N ALA* 3.4 11.4 - - - +
655N ALA* 3.3 7.9 - - + +
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Residues in contact with GLU 620 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616N ARG* 2.7 27.1 + - + +
617N ALA* 2.6 16.5 + - - +
619N VAL* 1.3 73.1 - - - +
621N SER* 1.3 63.5 + - - +
622N LEU 2.9 1.4 + - - -
623N GLY* 3.1 11.3 + - - -
624N PHE* 4.3 5.3 + - + -
650N TYR* 6.0 0.7 - - + -
651N GLY* 3.6 25.6 - - - +
654N MET* 4.0 21.8 - - + -
655N ALA* 3.2 12.9 - - - +
658N ILE* 4.6 7.4 - - + +
767N THR* 6.5 1.8 - - - -
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Residues in contact with SER 621 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583N MET* 3.7 44.4 - - - -
584N TYR* 4.0 9.0 - - - -
587N ALA* 4.0 9.3 - - - +
602N LEU* 5.0 4.2 - - - +
617N ALA 2.7 12.9 + - - -
618N ALA 4.1 1.3 - - - -
620N GLU* 1.3 72.7 - - - +
622N LEU* 1.3 66.3 + - - +
624N PHE* 3.0 32.5 + - - +
625N ILE* 3.5 4.9 + - - +
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Residues in contact with LEU 622 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599N ILE* 4.0 21.5 - - + -
602N LEU* 3.5 40.4 - - + -
603N LEU* 3.9 24.0 - - + +
606N ALA* 6.1 1.1 - - + -
618N ALA 3.1 15.2 + - - +
619N VAL* 3.1 33.4 - - + +
620N GLU 2.9 0.8 + - - -
621N SER* 1.3 73.9 - - - +
623N GLY* 1.3 51.1 + - - +
624N PHE 2.6 4.5 + - - -
625N ILE* 2.9 4.6 + - - -
626N LEU* 2.4 53.6 + - + +
637N VAL* 6.3 1.6 - - + -
640N LEU* 4.8 4.7 - - + -
655N ALA* 4.7 1.6 - - + -
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Residues in contact with GLY 623 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620N GLU 3.1 7.4 + - - -
622N LEU* 1.3 75.8 - - - +
624N PHE* 1.3 64.2 + - - +
626N LEU* 3.6 12.7 - - - +
627N PHE* 2.8 26.0 + - - +
633N CYS* 5.5 2.0 - - - -
655N ALA* 3.4 27.5 - - - +
658N ILE* 4.3 8.0 - - - +
659N CYS* 4.5 6.3 - - - +
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Residues in contact with PHE 624 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584N TYR* 6.1 4.3 - + - -
587N ALA* 3.7 21.1 - - + -
588N MET* 6.3 0.9 - - + -
591N CYS* 3.5 17.5 - - + -
592N GLY 2.4 29.8 + - - -
620N GLU* 4.8 2.9 - - + -
621N SER* 3.0 21.9 + - - +
622N LEU 2.6 5.3 + - - -
623N GLY* 1.3 77.8 - - - +
625N ILE* 1.3 53.3 + - - +
626N LEU 2.9 3.4 - - - -
627N PHE* 2.8 17.6 + - + +
658N ILE* 3.4 45.3 - - + -
748N LEU* 5.5 8.5 - - + -
760N VAL* 4.8 20.6 - - + -
763N VAL* 4.0 22.7 - - + -
764N LEU* 4.8 13.2 - - + -
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Residues in contact with ILE 625 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587N ALA* 4.8 4.7 - - - +
590N TYR* 3.1 41.1 - - + +
591N CYS* 3.5 1.6 - - - +
592N GLY 2.6 16.7 - - - +
594N GLY* 3.0 22.4 + - - -
595N ASN 3.3 33.2 - - - +
598N ALA* 4.7 3.8 - - + -
599N ILE* 5.2 5.6 - - + +
602N LEU* 4.7 14.1 - - + -
621N SER 3.5 4.1 + - - +
622N LEU* 2.9 6.3 + - + +
624N PHE* 1.3 77.0 - - - +
626N LEU* 1.3 59.4 + - + +
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Residues in contact with LEU 626 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K PHE* 6.4 1.8 - - + -
594N GLY* 5.0 7.0 - - - -
599N ILE* 4.6 21.8 - - + -
622N LEU* 2.4 63.7 + - + +
623N GLY* 3.4 8.3 - - - +
625N ILE* 1.3 76.9 - - + +
627N PHE* 1.3 60.0 + - - +
628N ARG 3.4 2.0 - - - -
629N THR* 2.6 35.4 - - - +
630N PRO* 3.8 1.6 - - - +
633N CYS* 5.5 11.2 - - + -
636N VAL* 4.9 21.5 - - + -
659N CYS* 4.6 2.4 - - - +
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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