Contacts of the helix formed by residues 592 - 605 (chain B) in PDB entry 3GTL
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 592 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576B ASP 4.8 4.0 + - - -
590B HIS* 2.5 22.4 + - - -
591B ARG* 1.3 72.6 - - + +
593B PRO* 1.3 65.9 - - - +
594B ALA* 3.1 28.1 + - - +
595B ARG* 3.2 35.7 + - - +
596B LEU* 4.0 5.0 + - - +
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Residues in contact with PRO 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ASP 5.3 3.6 - - - +
578B THR* 3.2 41.5 - - + +
590B HIS* 3.7 10.5 - - + +
591B ARG 4.2 0.9 - - - -
592B ASN* 1.3 86.5 - - - +
594B ALA* 1.3 64.7 + - + +
595B ARG 3.3 1.8 - - - -
596B LEU* 3.8 11.4 - - + -
597B MET* 3.1 27.5 + - - +
617B ARG* 3.5 32.5 + - - +
624B LEU* 5.0 4.7 - - + -
61I ASP* 4.6 7.0 - - - +
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Residues in contact with ALA 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B ASN* 3.1 14.3 + - - +
593B PRO* 1.3 81.7 - - + +
595B ARG* 1.3 64.3 + - + +
597B MET* 4.7 2.1 - - - +
598B GLU* 4.0 14.4 + - - +
617B ARG* 4.2 4.7 - - - +
61I ASP* 3.5 24.7 - - - +
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Residues in contact with ARG 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B ASN* 3.2 30.0 + - - +
594B ALA* 1.3 82.5 - - - +
596B LEU* 1.3 66.5 + - - +
597B MET 3.1 2.0 - - - -
598B GLU* 3.4 16.1 + - + +
599B THR* 3.0 29.2 + - - +
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Residues in contact with LEU 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B PHE* 5.1 2.9 - - + -
558B LEU* 3.9 22.0 - - + +
561B TRP* 4.9 23.3 - - + +
563B MET* 6.2 0.9 - - + -
580B VAL* 4.6 4.9 - - + -
590B HIS* 3.7 52.9 - - + +
592B ASN 4.0 4.2 + - - +
593B PRO* 3.4 7.6 + - + +
595B ARG* 1.3 77.0 - - - +
597B MET* 1.3 56.5 + - - +
599B THR* 4.3 3.9 - - + -
600B LEU* 3.1 42.6 + - + +
624B LEU* 4.1 23.1 - - + -
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Residues in contact with MET 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B PRO 3.1 16.0 + - - +
594B ALA 4.7 3.1 - - - +
595B ARG 3.1 0.6 - - - -
596B LEU* 1.3 74.2 - - - +
598B GLU* 1.3 68.0 + - - +
599B THR 3.0 1.8 - - - -
600B LEU* 2.9 10.6 + - - +
601B ARG* 2.8 55.9 + - - +
615B MET* 3.1 51.4 - - + +
617B ARG* 3.6 34.1 - - + +
624B LEU* 3.8 28.9 - - + -
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Residues in contact with GLU 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ALA 4.0 13.9 + - - +
595B ARG* 3.4 20.1 + - + +
597B MET* 1.3 75.4 - - - +
599B THR* 1.3 55.5 + - - +
601B ARG* 3.7 11.1 - - - +
602B THR* 2.7 42.4 + - - +
641B GLU* 4.4 13.0 - - - +
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Residues in contact with THR 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B PHE* 4.0 26.0 - - + -
561B TRP* 4.4 24.1 - - + -
595B ARG* 3.0 17.5 + - - +
596B LEU* 4.3 5.4 - - + +
597B MET 2.9 1.2 + - - -
598B GLU* 1.3 75.2 - - - +
600B LEU* 1.3 67.3 + - + +
601B ARG 3.0 1.6 - - - -
602B THR* 2.8 19.2 + - - -
603B LEU* 3.1 22.9 + - + +
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Residues in contact with LEU 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B ILE* 5.0 14.8 - - + -
557B PHE* 3.6 31.9 - - + -
558B LEU* 4.4 6.7 - - + -
596B LEU* 3.1 38.3 + - + +
597B MET* 2.9 17.9 + - - +
599B THR* 1.3 73.6 - - + +
601B ARG* 1.3 60.9 + - - +
603B LEU* 3.9 7.6 + - + +
604B ARG* 3.8 9.0 + - - +
609B ILE* 5.2 4.5 - - + +
615B MET* 3.3 45.0 - - + +
624B LEU* 5.5 1.8 - - + -
626B ILE* 4.1 28.0 - - + -
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Residues in contact with ARG 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B MET* 2.8 55.4 + - - +
598B GLU* 3.7 9.5 - - - +
600B LEU* 1.3 68.0 - - - +
602B THR* 1.3 58.0 + - - +
603B LEU 3.0 1.8 - - - -
604B ARG* 2.7 39.7 + - - +
605B ARG* 2.9 39.0 + - - +
615B MET* 3.7 18.5 + - + +
617B ARG* 5.2 6.7 - - - +
691B GLU* 4.5 6.7 + - - +
697B GLU* 5.0 9.3 + - - -
700B SER* 4.9 11.1 + - - -
701B ILE* 6.1 2.0 - - - +
739B THR* 6.2 1.6 - - - +
740B HIS* 5.9 4.9 - - - -
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Residues in contact with THR 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598B GLU* 2.7 29.4 + - - +
599B THR* 2.8 10.4 + - - -
601B ARG* 1.3 76.6 - - - +
603B LEU* 1.3 65.1 + - + +
605B ARG* 3.9 8.8 - - - +
606B LYS* 3.4 42.2 + - - +
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Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B PHE* 4.0 34.8 - - + -
599B THR* 3.5 20.9 - - + +
600B LEU* 4.3 6.1 - - + +
601B ARG 2.8 1.2 + - - -
602B THR* 1.3 82.4 - - + +
604B ARG* 1.3 58.6 + - - +
606B LYS* 3.6 3.0 + - + +
607B GLY 3.0 4.2 + - - -
608B ASP* 2.6 50.8 + - + +
609B ILE* 2.9 36.2 + - + +
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Residues in contact with ARG 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B LEU 3.8 9.9 + - - +
601B ARG* 2.7 20.4 + - - +
603B LEU* 1.3 69.7 - - - +
605B ARG* 1.3 53.7 + - - +
606B LYS 3.0 4.3 - - - -
607B GLY* 2.8 22.3 + - - -
609B ILE* 3.1 14.4 + - + +
610B ASN 3.6 19.1 - - - +
611B PRO* 3.8 19.7 + - + +
613B VAL 3.6 19.9 + - - +
614B SER* 3.8 1.8 - - - +
615B MET* 3.8 23.4 - - + +
685B LEU 4.6 3.3 - - - +
691B GLU* 2.8 52.0 + - - +
692B TYR 3.2 23.6 + - - +
693B ILE* 4.9 0.4 - - - +
697B GLU* 2.7 40.0 + - - -
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Residues in contact with ARG 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B ARG* 2.9 40.9 + - - +
602B THR* 3.9 7.9 - - - +
604B ARG* 1.3 73.9 - - - +
606B LYS* 1.3 58.1 + - - +
639B ILE* 3.1 39.3 - - + +
641B GLU* 3.5 33.3 + - - +
652B LYS* 4.9 16.4 + - - +
685B LEU 4.7 2.5 - - - -
686B ASN 3.5 3.9 - - - +
687B GLU 3.9 2.3 - - - +
688B GLY* 3.3 29.2 + - - -
691B GLU* 2.9 46.0 + - + +
739B THR* 5.4 3.2 + - - -
740B HIS* 4.3 8.1 + - - -
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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