Contacts of the helix formed by residues 612 - 626 (chain B) in PDB entry 1GGE
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 ARG 612 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610B GLU 4.2 2.5 - - - -
611B VAL* 1.3 72.0 - - - +
613B SER* 1.3 64.3 + - - +
614B ALA* 3.1 5.4 - - + +
615B ASP* 2.7 34.9 + - - +
616B LEU 3.6 2.8 + - - -
643B ASP* 3.4 23.5 + - - +
669B CYS* 3.0 37.0 + - + +
670B GLY* 3.4 32.1 + - - +
700B ASP* 5.1 4.0 + - - -
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Residues in contact with SER 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B VAL* 2.8 12.6 + - - -
612B ARG* 1.3 69.0 - - - +
614B ALA* 1.3 62.1 + - - -
615B ASP 3.2 0.3 + - - -
616B LEU* 3.3 7.0 + - - +
617B LEU* 3.0 32.4 + - - +
642B ALA* 3.9 9.4 - - - -
643B ASP* 2.7 23.1 + - - -
644B ASP* 3.3 33.0 + - - +
646B THR* 4.5 3.8 - - - -
648B LEU* 6.5 0.7 - - - -
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Residues in contact with ALA 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ARG* 2.8 8.4 + - + +
613B SER* 1.3 77.7 + - - +
615B ASP* 1.3 65.9 + - - +
617B LEU* 3.7 11.6 + - - +
618B ALA* 3.3 20.1 + - - +
643B ASP* 5.0 1.2 + - - +
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Residues in contact with ASP 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ARG* 2.7 22.4 + - - +
614B ALA* 1.3 71.9 - - - +
616B LEU* 1.3 58.9 + - - +
618B ALA* 3.1 4.2 + - - +
619B ILE* 2.7 33.2 + - + +
668B PRO* 3.9 15.5 - - + -
669B CYS* 3.0 35.3 + - - +
698B ALA* 3.6 6.3 - - - +
722B ASP 5.3 0.2 - - - +
723B SER* 3.6 12.1 - - - -
724B ALA* 2.9 38.2 + - + -
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Residues in contact with LEU 616 (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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605B ILE* 3.8 41.7 - - + -
607B LEU* 4.4 7.2 - - + -
611B VAL* 4.1 14.8 - - + -
612B ARG 3.6 2.8 + - - -
613B SER* 3.3 11.2 + - - +
615B ASP* 1.3 77.7 - - - +
617B LEU* 1.3 56.0 + - - +
619B ILE* 4.1 7.8 - - + +
620B LEU* 2.7 56.9 + - + +
632B LEU* 4.4 9.2 - - + -
648B LEU* 3.5 44.0 - - + -
668B PRO* 4.8 2.6 - - + +
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Residues in contact with LEU 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B SER* 3.0 23.9 + - - +
614B ALA* 3.8 10.5 - - - +
616B LEU* 1.3 75.7 - - - +
618B ALA* 1.3 64.1 + - - +
620B LEU* 4.3 2.6 - - - +
621B LYS* 3.0 29.3 + - - +
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Residues in contact with ALA 618 (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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614B ALA 3.3 10.3 + - - +
615B ASP 3.1 6.7 + - - +
617B LEU* 1.3 75.0 - - - +
619B ILE* 1.3 68.8 + - - +
621B LYS* 4.0 5.1 - - - +
622B ALA* 3.3 23.6 + - - +
724B ALA 3.3 25.8 - - - +
725B ASP* 4.4 9.9 - - - -
726B GLY 5.2 0.2 - - - +
729B MET* 4.0 3.5 - - - +
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Residues in contact with ILE 619 (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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605B ILE* 3.9 22.4 - - + -
615B ASP 2.7 31.7 + - - +
616B LEU* 3.6 10.5 - - + +
618B ALA* 1.3 74.9 - - - +
620B LEU* 1.3 64.2 + - - +
622B ALA* 3.3 2.4 + - - +
623B LEU* 3.1 30.0 + - + +
666B ILE* 3.7 46.2 - - + -
668B PRO* 4.0 20.4 - - + -
724B ALA* 3.8 19.7 - - + -
728B PHE* 5.7 0.2 - - + -
729B MET* 3.8 16.7 - - + +
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ILE* 3.7 25.1 - - + -
616B LEU* 2.7 47.9 + - + +
617B LEU* 4.3 2.9 - - - +
619B ILE* 1.3 73.8 - - - +
621B LYS* 1.3 60.4 + - - +
623B LEU* 3.4 6.5 + - + +
624B LYS* 3.0 27.0 + - - +
630B ALA* 3.7 17.9 - - + -
632B LEU* 4.8 11.9 - - + -
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Residues in contact with LYS 621 (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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617B LEU 3.0 19.9 + - - +
618B ALA* 4.0 5.2 - - - +
620B LEU* 1.3 75.1 - - - +
622B ALA* 1.3 59.5 + - - +
624B LYS* 3.5 5.6 + - - +
625B ALA* 3.1 26.7 + - + +
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Residues in contact with ALA 622 (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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618B ALA 3.3 15.9 + - - +
619B ILE 3.8 2.2 - - - +
621B LYS* 1.3 79.1 - - - +
623B LEU* 1.3 65.3 + - - +
625B ALA* 3.3 15.6 + - - +
626B LYS* 3.5 16.1 + - - +
726B GLY* 6.2 1.3 - - - -
729B MET* 3.7 28.9 - - + -
730B ASP* 6.1 0.4 - - - +
733B LEU* 3.9 9.2 - - + +
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Residues in contact with LEU 623 (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* 4.0 22.0 - - + -
605B ILE* 4.4 1.3 - - + -
619B ILE* 3.1 37.0 + - + +
620B LEU* 3.8 8.1 - - + +
622B ALA* 1.3 74.9 - - - +
624B LYS* 1.3 62.7 + - - +
626B LYS* 3.0 9.5 + - - -
628B VAL* 2.9 58.5 + - + +
629B HIS 4.5 2.0 - - - +
630B ALA* 3.9 27.4 - - + -
666B ILE* 4.6 1.3 - - + -
729B MET* 3.8 17.7 - - + -
732B LEU* 4.8 2.9 - - + -
733B LEU* 4.2 13.2 - - + -
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Residues in contact with LYS 624 (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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620B LEU 3.0 18.4 + - - +
621B LYS* 3.8 6.1 - - - +
623B LEU* 1.3 76.4 - - - +
625B ALA* 1.3 60.2 + - - +
627B GLY* 3.2 12.7 + - - +
628B VAL 4.1 4.2 + - - -
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Residues in contact with ALA 625 (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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621B LYS* 3.1 14.9 + - + +
622B ALA* 3.6 11.0 - - - +
623B LEU 3.2 0.6 - - - -
624B LYS* 1.3 77.2 - - - +
626B LYS* 1.3 67.4 + - + +
627B GLY 3.9 0.2 + - - -
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Residues in contact with LYS 626 (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 VAL* 3.8 23.6 - - + +
599B LYS* 3.5 20.3 - - - +
622B ALA 3.5 4.0 + - - +
623B LEU 3.0 7.9 + - - +
625B ALA* 1.3 84.5 - - - +
627B GLY* 1.3 61.9 + - - +
628B VAL* 3.4 6.2 + - + -
730B ASP* 5.2 7.2 + - - +
733B LEU* 3.8 38.6 - - + +
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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