Contacts of the helix formed by residues 634 - 648 (chain F) in PDB entry 5G04
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 HIS 634 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479F TYR* 5.0 7.4 - - - -
507F ARG* 6.0 3.4 - - - -
601F ALA* 4.2 12.7 - - + +
602F TYR* 3.3 35.5 - + + -
605F THR* 2.8 29.1 + - - -
627F ALA* 4.9 2.2 - - - +
628F ILE* 4.6 0.2 - - - +
631F ASN* 3.3 39.2 + - + +
632F PRO 3.5 0.8 - - - -
633F ARG* 1.3 75.1 - - - +
635F TYR* 1.3 64.2 + - - +
636F ASN* 3.1 32.8 + - + -
637F ALA* 3.3 18.4 + - - +
638F TRP* 3.9 7.2 + - - -
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Residues in contact with TYR 635 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F TYR* 3.5 24.9 - + - -
510F PHE* 5.4 3.8 - - - -
511F GLU* 2.7 35.0 + - - -
633F ARG 3.5 3.4 + - - -
634F HIS* 1.3 71.8 - - - +
636F ASN* 1.3 89.7 + - - +
638F TRP* 2.6 34.9 + - - +
639F TYR* 2.8 13.9 + - + -
661F ALA* 3.9 22.2 - - + +
664F ILE* 4.1 10.8 - - + -
665F ASN* 3.5 19.9 + - + -
668F SER* 4.7 2.4 + - - -
671F LEU* 3.9 27.1 - - + -
498R ILE* 4.3 21.0 - - + +
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Residues in contact with ASN 636 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F TYR* 5.2 0.2 + - - -
510F PHE* 5.0 5.0 - - - -
511F GLU* 4.4 5.5 + - - +
602F TYR* 3.7 21.0 + - - -
605F THR* 3.5 21.7 - - + +
609F HIS* 4.1 6.2 + - - -
634F HIS* 3.1 23.3 + - + -
635F TYR* 1.3 115.6 + - - +
637F ALA* 1.3 57.9 + - - +
639F TYR* 3.5 8.7 - - - +
640F GLY* 3.0 22.3 + - - -
498R ILE* 4.1 23.0 - - + +
499R ARG* 5.8 0.9 - - - +
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Residues in contact with ALA 637 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605F THR* 4.2 5.3 - - - +
624F PHE* 3.5 19.4 - - + +
627F ALA* 3.2 36.1 - - + -
628F ILE* 3.6 16.6 - - + +
634F HIS* 3.3 9.0 + - - +
635F TYR 3.0 0.4 - - - -
636F ASN* 1.3 77.0 - - - +
638F TRP* 1.3 55.9 + - - +
640F GLY* 3.0 2.1 + - - -
641F LEU* 2.8 36.2 + - - +
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Residues in contact with TRP 638 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625F ARG* 4.7 7.6 - - - -
628F ILE* 3.6 35.9 - - + +
632F PRO 2.8 23.4 + - - -
634F HIS 4.0 9.9 - - - -
635F TYR 2.6 15.7 + - - +
637F ALA* 1.3 73.4 - - - +
639F TYR* 1.3 58.2 - - - +
641F LEU* 3.4 25.7 - - + +
642F GLY 3.3 15.4 + - - -
657F HIS* 3.6 44.7 - + - +
660F LYS* 3.5 32.5 - - + +
661F ALA* 3.7 17.9 - - + -
664F ILE* 3.5 23.4 - - + +
526Y GLN* 3.4 26.5 - - - -
530Y ASP* 5.1 12.8 - - + -
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Residues in contact with TYR 639 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609F HIS* 4.2 5.4 - + - -
635F TYR* 2.8 10.6 + - + +
636F ASN* 3.5 9.0 - - - +
638F TRP* 1.3 74.0 - - - +
640F GLY* 1.3 68.4 + - - +
642F GLY 3.2 2.1 + - - -
643F MET* 3.0 46.3 + - + +
658F PHE* 3.3 38.4 - + - -
661F ALA* 4.0 3.2 - - + +
671F LEU* 3.6 26.2 - - + -
674F HIS* 3.1 42.9 + + + -
496R GLN 4.8 3.6 + - - -
497R GLY 4.7 3.6 + - - -
498R ILE* 3.4 49.5 - - + +
499R ARG 5.6 0.4 - - - -
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Residues in contact with GLY 640 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609F HIS* 4.7 0.4 - - - -
624F PHE* 3.6 30.5 - - - -
636F ASN 3.0 9.1 + - - -
637F ALA 3.0 8.7 + - - -
639F TYR* 1.3 78.7 - - - +
641F LEU* 1.3 63.3 + - - +
643F MET* 3.1 11.1 + - - +
644F ILE* 3.0 24.9 + - - +
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Residues in contact with LEU 641 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621F LEU* 4.2 14.6 - - + +
624F PHE* 3.8 23.8 - - + -
625F ARG* 3.9 36.3 - - + +
628F ILE* 3.8 21.8 - - + -
637F ALA 2.8 14.9 + - - +
638F TRP* 3.4 39.7 - - + +
640F GLY* 1.3 69.5 - - - +
642F GLY* 1.3 58.2 + - - +
644F ILE* 3.1 8.2 + - - +
645F TYR* 2.9 38.3 + - + -
657F HIS* 3.9 13.0 - - + +
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Residues in contact with GLY 642 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638F TRP 3.3 3.2 + - - -
639F TYR 3.2 7.2 + - - -
640F GLY 3.2 1.0 - - - -
641F LEU* 1.3 75.9 - - - +
643F MET* 1.3 53.7 + - - +
645F TYR* 3.1 4.4 + - - +
646F TYR* 2.7 35.3 + - - +
654F ALA* 3.7 10.1 - - - +
657F HIS* 3.7 21.5 - - - +
658F PHE* 3.6 16.2 - - - -
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Residues in contact with MET 643 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609F HIS* 4.0 21.8 - - + +
612F VAL* 3.7 40.4 - - + -
624F PHE* 5.0 0.2 - - + -
639F TYR* 3.0 39.5 + - + +
640F GLY* 3.1 10.5 + - - +
642F GLY* 1.3 72.8 - - - +
644F ILE* 1.3 57.5 + - - +
646F TYR* 3.1 9.6 + - + +
647F LYS* 2.9 48.8 + - + +
658F PHE* 3.4 12.9 - - + -
674F HIS* 5.3 7.9 - - + -
495R HIS* 5.7 9.0 - - + -
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Residues in contact with ILE 644 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612F VAL* 3.8 17.7 - - + -
617F LEU* 3.5 29.8 - - + +
620F ALA* 3.7 8.5 - - + -
621F LEU* 3.6 34.5 - - + +
624F PHE* 3.3 33.4 - - + -
640F GLY 3.0 16.6 + - - +
641F LEU 3.5 5.4 - - - +
643F MET* 1.3 76.8 - - + +
645F TYR* 1.3 61.7 + - - +
647F LYS* 3.4 8.3 + - + +
648F GLN* 3.0 40.1 + - - +
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Residues in contact with TYR 645 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621F LEU* 3.8 32.5 - - + +
625F ARG* 4.7 4.7 + - - -
641F LEU* 2.9 31.0 + - + -
642F GLY 3.7 5.2 - - - +
644F ILE* 1.3 73.3 - - - +
646F TYR* 1.3 60.0 + - - +
648F GLN* 3.4 11.9 + - - +
649F GLU 3.0 20.6 + - - -
650F LYS* 3.1 36.2 + - + +
653F LEU* 3.7 23.3 - - + -
654F ALA* 4.2 17.7 - - - +
657F HIS* 3.2 36.8 - + - -
529Y MET* 4.1 22.9 - - + +
549Y MET* 4.5 14.2 - - - +
552Y MET* 5.4 2.0 - - + -
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Residues in contact with TYR 646 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642F GLY 2.7 16.8 + - - +
643F MET* 3.1 16.8 + - + +
645F TYR* 1.3 74.7 - - - +
647F LYS* 1.3 69.2 + - + +
649F GLU* 2.9 22.0 + - - +
651F PHE* 3.7 32.3 - + - -
654F ALA* 3.8 10.5 - - + +
658F PHE* 4.7 4.5 - + + -
674F HIS* 5.5 6.1 - + - -
677F VAL* 4.1 28.4 - - + +
678F VAL* 3.7 26.7 - - + -
681F ALA* 5.2 1.3 - - + -
780F ASP* 4.1 20.8 - - - +
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Residues in contact with LYS 647 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612F VAL* 3.9 24.8 - - + +
613F LEU* 5.6 3.8 - - - +
615F GLU* 4.1 25.3 + - - +
617F LEU* 5.2 12.9 - - + +
643F MET* 2.9 31.3 + - + +
644F ILE* 3.9 7.4 - - - +
646F TYR* 1.3 87.9 - - + +
648F GLN* 1.3 60.9 + - - +
649F GLU* 3.1 9.2 + - - +
495R HIS* 6.2 1.4 + - - -
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Residues in contact with GLN 648 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617F LEU* 3.9 25.5 - - + +
618F ASP* 3.3 25.7 + - - -
621F LEU* 3.9 20.4 - - - +
644F ILE* 3.0 33.4 + - - +
645F TYR* 3.7 15.1 - - - +
646F TYR 3.3 0.2 - - - -
647F LYS* 1.3 73.6 - - - +
649F GLU* 1.3 65.0 + - - +
650F LYS* 3.3 33.1 + - - +
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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