Contacts of the helix formed by residues 592 - 607 (chain A) in PDB entry 4GDF
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 ILE 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A THR* 3.5 21.3 - - + -
365A PHE* 4.1 28.5 - - + -
366A ASN* 3.3 39.3 - - - +
369A LEU* 4.8 7.4 - - + -
588A PHE* 5.1 3.6 - - + -
589A ALA* 3.2 13.2 + - + +
590A GLN 3.1 0.8 - - - -
591A SER* 1.3 81.0 + - - +
593A GLN* 1.3 66.1 + - - +
594A SER* 3.0 3.4 - - - +
595A ARG* 3.1 23.8 + - - +
596A ILE* 3.1 30.8 + - + +
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Residues in contact with GLN 593 (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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585A VAL* 2.8 39.8 - - + +
586A ALA* 3.6 10.8 + - - +
588A PHE* 3.5 12.6 + - + +
589A ALA 3.0 19.2 + - - +
590A GLN* 3.0 35.0 + - - +
592A ILE* 1.3 74.7 - - - +
594A SER* 1.3 66.5 + - - +
596A ILE* 3.5 9.6 - - - +
597A VAL* 2.9 31.8 + - + +
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Residues in contact with SER 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLN 4.6 2.9 + - - -
591A SER 4.1 12.6 + - - -
592A ILE 4.6 1.1 - - - -
593A GLN* 1.3 80.0 + - - +
595A ARG* 1.3 66.5 + - - +
597A VAL* 3.2 6.7 + - - +
598A GLU* 3.1 30.9 + - - +
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Residues in contact with ARG 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASN* 2.7 48.0 + - - +
369A LEU* 3.7 32.9 - - + +
370A ASP* 2.7 29.9 + - - -
373A ASP* 3.2 24.0 + - - -
592A ILE* 3.1 17.2 + - + +
594A SER* 1.3 75.7 - - - +
596A ILE* 1.3 57.0 + - - +
598A GLU* 3.2 11.4 + - - +
599A TRP* 2.7 46.1 + - + +
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Residues in contact with ILE 596 (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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365A PHE* 5.6 0.7 - - + -
369A LEU* 4.4 12.3 - - + -
576A LEU* 5.5 1.8 - - + -
580A ILE* 3.2 32.8 - - + +
585A VAL* 4.6 11.0 - - + -
588A PHE* 3.7 53.8 - - + -
592A ILE* 3.1 29.6 + - + +
593A GLN* 3.2 10.1 + - - +
595A ARG* 1.3 74.9 - - - +
597A VAL* 1.3 52.8 + - - +
599A TRP* 3.7 4.5 - - + +
600A LYS* 2.7 44.1 + - + +
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Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A VAL* 3.4 29.6 - - + -
593A GLN* 2.9 18.3 + - + +
594A SER* 3.5 8.5 - - - +
596A ILE* 1.3 74.2 - - - +
598A GLU* 1.3 61.9 + - + +
600A LYS* 3.1 8.4 + - + +
601A GLU* 2.9 45.1 + - + +
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Residues in contact with GLU 598 (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 SER* 3.1 20.9 + - - +
595A ARG* 3.7 11.0 - - - +
597A VAL* 1.3 77.4 - - + +
599A TRP* 1.3 58.0 + - + +
601A GLU* 3.6 13.4 + - - +
602A ARG* 3.1 24.8 + - - +
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Residues in contact with TRP 599 (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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369A LEU* 3.6 38.0 - - + +
372A MET* 3.8 29.6 - - + -
373A ASP* 3.4 30.1 + - - -
376A PHE* 3.5 32.1 - + + -
384A ILE* 4.7 2.7 - - + -
577A LEU* 4.7 3.1 - - + -
580A ILE* 4.1 15.9 - - + -
595A ARG* 2.7 29.7 + - + +
596A ILE* 3.7 4.9 - - - +
598A GLU* 1.3 70.1 - - + +
600A LYS* 1.3 67.7 + - - +
602A ARG* 3.0 51.9 + - + +
603A LEU* 3.1 27.9 + - + +
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Residues in contact with LYS 600 (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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580A ILE* 3.1 32.7 - - - +
581A TRP* 4.9 7.4 - - + -
582A TYR 5.2 0.6 - - - -
583A ARG 2.5 28.7 + - - -
584A PRO* 3.5 4.4 - - - +
585A VAL* 3.3 36.2 - - + +
588A PHE* 5.1 1.0 - - - -
596A ILE* 2.7 24.2 + - + +
597A VAL* 3.4 7.0 - - - +
599A TRP* 1.3 76.2 - - - +
601A GLU* 1.3 58.1 + - + +
603A LEU* 3.1 14.7 + - + +
604A ASP* 2.7 31.2 - - - +
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Residues in contact with GLU 601 (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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597A VAL* 2.9 30.4 + - + +
598A GLU* 3.8 11.8 - - - +
600A LYS* 1.3 76.5 - - + +
602A ARG* 1.3 62.5 + - - +
604A ASP* 3.3 21.6 + - + +
605A LYS* 3.4 14.6 + - - +
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Residues in contact with ARG 602 (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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376A PHE* 3.4 34.7 + - - +
384A ILE* 3.9 23.1 - - + +
598A GLU 3.1 14.4 + - - +
599A TRP* 3.0 46.4 + - + +
601A GLU* 1.3 79.1 - - - +
603A LEU* 1.3 61.5 + - - +
605A LYS* 3.7 10.3 + - - +
606A GLU* 3.4 35.1 + - - +
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Residues in contact with LEU 603 (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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384A ILE* 4.1 18.4 - - + -
388A MET* 3.4 28.9 - - + -
577A LEU* 4.2 14.6 - - + +
580A ILE* 4.0 31.6 - - + -
581A TRP* 3.5 37.5 - - + +
599A TRP* 3.4 18.6 - - + +
600A LYS* 3.1 7.0 + - - +
602A ARG* 1.3 74.1 - - - +
604A ASP* 1.3 57.2 + - - +
606A GLU* 4.4 4.0 - - - -
607A PHE* 2.7 41.6 + - + +
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Residues in contact with ASP 604 (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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581A TRP* 4.2 12.9 - - - -
600A LYS* 2.7 29.8 - - - +
601A GLU* 3.4 18.4 - - + +
603A LEU* 1.3 77.4 - - - +
605A LYS* 1.3 61.0 + - - +
607A PHE 3.3 18.2 - - - +
608A SER* 4.0 5.9 + - - -
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Residues in contact with LYS 605 (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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601A GLU 3.4 9.9 + - - +
602A ARG* 3.9 13.5 - - - +
604A ASP* 1.3 80.8 - - - +
606A GLU* 1.3 73.6 + - + +
607A PHE* 4.7 0.7 - - - -
608A SER* 4.8 2.1 + - - -
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Residues in contact with GLU 606 (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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384A ILE* 3.1 33.0 - - + +
385A GLU* 6.1 0.5 - - - +
602A ARG* 3.4 36.9 + - - +
603A LEU* 3.4 1.3 + - - +
605A LYS* 1.3 88.8 - - + +
607A PHE* 1.3 82.4 + - + +
608A SER 4.1 1.2 + - - -
611A VAL* 4.5 8.5 - - - +
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Residues in contact with PHE 607 (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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384A ILE* 3.6 16.8 - - + -
385A GLU* 3.5 46.0 - - + -
388A MET* 3.5 48.2 - - + -
581A TRP* 3.5 22.0 - + + -
603A LEU* 2.7 24.5 + - + +
604A ASP* 3.3 11.7 - - - +
606A GLU* 1.3 93.1 - - + +
608A SER* 1.3 68.0 + - - +
611A VAL* 4.0 21.3 - - + -
612A TYR* 4.4 7.9 - - + -
615A MET* 4.1 10.8 - - + -
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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