Contacts of the helix formed by residues 600 - 615 (chain B) in PDB entry 2G5T
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 THR 600 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ILE* 4.4 0.5 - - - +
597B ARG* 2.7 29.7 + - + +
599B GLY* 1.3 84.5 - - - +
601B PHE* 1.3 80.0 + - - -
602B GLU* 2.9 5.0 + - - -
603B VAL* 2.8 20.7 - - - +
604B GLU* 2.9 28.9 + - - +
682B HIS* 3.5 28.5 - - + -
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Residues in contact with PHE 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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581B ARG* 3.5 53.2 - - + +
593B ALA* 3.2 32.1 - - + -
594B ILE* 3.8 4.3 - - + -
597B ARG* 5.8 4.0 - - + -
600B THR* 1.3 88.4 + - - +
602B GLU* 1.3 61.3 + - - +
604B GLU* 3.8 22.7 - - - -
605B ASP* 2.9 36.6 + - - +
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Residues in contact with GLU 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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548B ALA* 3.6 32.1 - - + +
580B GLY* 5.6 1.1 - - - -
581B ARG 3.6 22.0 - - - +
594B ILE* 3.8 18.5 - - + +
598B LEU* 3.6 2.5 - - - +
599B GLY* 2.6 28.5 + - - -
600B THR 2.9 19.7 + - - -
601B PHE* 1.3 75.3 + - - +
603B VAL* 1.3 59.2 + - - +
605B ASP* 4.7 3.1 - - - +
606B GLN* 3.5 24.8 + - - +
631B TYR* 2.6 29.0 + - + +
634B TYR* 4.4 0.5 - - - -
635B VAL* 4.2 9.3 - - + +
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Residues in contact with VAL 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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599B GLY* 3.3 31.4 - - - +
600B THR* 2.8 23.3 - - - +
602B GLU* 1.3 79.7 - - + +
604B GLU* 1.3 65.1 + - + +
606B GLN* 3.1 12.8 + - - +
607B ILE* 3.2 20.1 + - + +
634B TYR* 6.5 0.2 - - + -
635B VAL* 4.1 16.2 - - + -
638B MET* 4.1 16.4 - - + +
639B VAL* 3.5 33.7 - - + +
642B SER* 5.4 1.8 - - - -
691B ARG* 5.8 2.5 - - - +
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Residues in contact with GLU 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ARG* 4.5 4.8 + - - +
600B THR* 2.9 28.5 + - - +
601B PHE* 3.8 30.2 - - - +
603B VAL* 1.3 78.9 - - + +
605B ASP* 1.3 62.1 + - - +
607B ILE* 2.9 16.1 + - + +
608B GLU* 2.9 27.4 + - - +
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Residues in contact with ASP 605 (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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519B LEU* 4.8 12.1 - - + +
524B PHE* 5.8 0.9 - - - -
578B PHE* 3.4 22.1 - - + -
580B GLY* 4.1 6.7 - - - -
581B ARG* 2.5 64.9 + - - +
601B PHE 2.9 18.4 + - - +
602B GLU 4.7 2.5 - - - +
604B GLU* 1.3 75.7 - - - +
606B GLN* 1.3 57.6 + - - +
608B GLU* 3.7 9.8 - - - +
609B ALA* 2.8 30.5 + - - +
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Residues in contact with GLN 606 (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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544B LEU* 3.5 49.8 - - + +
546B VAL* 3.3 36.9 - - + +
548B ALA* 3.9 5.2 - - - +
578B PHE* 3.6 36.3 + - - +
580B GLY 5.0 2.4 + - - -
602B GLU 3.5 16.3 + - - +
603B VAL* 3.1 14.1 + - - +
605B ASP* 1.3 80.0 - - - +
607B ILE* 1.3 61.1 + - - +
609B ALA* 3.5 5.4 + - - +
610B ALA* 3.4 15.2 + - - +
626B ILE* 4.6 4.7 - - + -
635B VAL* 4.1 9.6 - - + -
639B VAL* 4.5 3.4 - - + -
647B PHE* 4.4 1.3 - - - -
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Residues in contact with ILE 607 (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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603B VAL* 3.5 21.1 - - + +
604B GLU* 2.9 13.7 + - + +
606B GLN* 1.3 74.2 - - - +
608B GLU* 1.3 65.4 + - - +
609B ALA 3.1 1.7 + - - -
610B ALA* 3.3 3.6 + - - +
611B ARG* 3.0 49.0 + - - +
639B VAL* 3.8 23.3 - - + -
642B SER* 3.4 34.1 - - - +
644B SER* 3.8 15.0 - - - +
646B VAL* 4.2 7.0 - - + +
647B PHE* 4.2 8.1 - - + -
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Residues in contact with GLU 608 (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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519B LEU* 3.8 19.9 - - + +
604B GLU 2.9 11.8 + - - +
605B ASP* 3.3 13.7 + - - +
607B ILE* 1.3 77.9 - - - +
609B ALA* 1.3 61.2 + - - +
611B ARG* 3.2 38.1 + - - +
612B GLN* 3.0 51.7 + - - +
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Residues in contact with ALA 609 (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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517B ILE* 4.5 10.8 - - + -
544B LEU* 5.5 0.4 - - + -
578B PHE* 3.5 40.4 - - + -
605B ASP 2.8 17.3 + - - +
606B GLN* 3.5 7.2 - - - +
607B ILE 3.1 0.2 - - - -
608B GLU* 1.3 77.6 - - - +
610B ALA* 1.3 57.9 + - - +
612B GLN* 3.1 5.5 + - - +
613B PHE* 2.8 40.8 + - + -
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Residues in contact with ALA 610 (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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542B LEU* 5.1 2.2 - - + -
544B LEU* 4.4 5.6 - - + -
606B GLN 3.4 3.5 + - - +
607B ILE 3.3 3.2 + - - +
609B ALA* 1.3 76.7 - - - +
611B ARG* 1.3 60.4 + - - +
613B PHE* 3.5 17.3 - - + +
614B SER* 2.9 30.1 + - - -
624B ILE* 4.2 13.9 - - + +
646B VAL* 4.3 7.8 - - + +
647B PHE* 3.6 36.1 - - + -
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Residues in contact with ARG 611 (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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604B GLU 5.7 0.2 + - - -
607B ILE* 3.0 41.2 + - - +
608B GLU* 3.2 43.2 + - - +
609B ALA 3.1 0.2 - - - -
610B ALA* 1.3 79.1 - - - +
612B GLN* 1.3 58.8 + - + +
614B SER* 2.8 19.5 + - - +
615B LYS* 3.7 15.4 + - + +
644B SER* 4.0 14.3 + - - +
646B VAL* 3.9 26.8 - - + +
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Residues in contact with GLN 612 (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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517B ILE* 4.2 31.4 - - + +
518B ILE 4.5 3.5 + - - +
519B LEU* 3.1 29.9 - - - +
608B GLU* 3.0 26.2 + - - +
609B ALA 3.1 6.0 + - - +
611B ARG* 1.3 77.7 - - + +
613B PHE* 1.3 66.5 + - + +
615B LYS* 3.2 15.4 + - - +
616B MET* 3.4 15.9 + - - +
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Residues in contact with PHE 613 (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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517B ILE* 5.1 5.8 - - + -
526B TYR* 3.7 55.4 - + + -
528B MET* 4.8 5.4 - - - -
542B LEU* 4.0 29.8 - - + -
544B LEU* 4.3 11.0 - - + -
576B ALA* 4.0 17.9 - - + -
578B PHE* 4.5 3.8 - + + -
609B ALA* 2.8 39.6 + - + +
610B ALA* 3.5 17.0 - - + +
612B GLN* 1.3 79.1 - - + +
614B SER* 1.3 62.0 + - - +
616B MET* 3.1 32.6 + - - +
619B VAL* 3.1 20.1 - - + +
624B ILE* 6.0 0.2 - - + -
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Residues in contact with SER 614 (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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539B LYS* 5.1 2.6 + - - -
610B ALA 2.9 14.4 + - - -
611B ARG* 2.8 26.2 + - - +
613B PHE* 1.3 77.0 - - - +
615B LYS* 1.3 65.7 + - - +
616B MET 3.3 2.9 + - - -
617B GLY* 3.9 6.2 + - - -
619B VAL* 3.6 26.6 - - - +
621B ASN* 3.6 29.7 + - - +
624B ILE* 3.7 12.1 - - - -
646B VAL* 5.6 1.7 - - - +
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Residues in contact with LYS 615 (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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611B ARG* 3.7 12.9 + - + +
612B GLN* 3.2 11.3 + - - +
613B PHE 3.2 1.0 - - - -
614B SER* 1.3 81.9 + - - +
616B MET* 1.3 61.9 + - - +
617B GLY 3.1 3.8 + - - -
621B ASN* 5.3 12.3 - - - +
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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