Contacts of the helix formed by residues 599 - 614 (chain B) in PDB entry 6FF7
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 GLU 599 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594B PRO* 4.8 4.3 - - - +
596B ASN* 3.8 17.4 + - + +
597B PRO 3.5 0.4 - - - -
598B SER* 1.3 74.6 - - - +
600B LEU* 1.3 61.4 + - - +
601B PRO 3.8 1.1 - - - -
602B LYS* 4.1 14.3 + - + +
603B MET* 4.0 14.9 + - - +
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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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594B PRO* 5.5 5.2 - - + -
597B PRO* 3.9 16.4 - - + +
598B SER 3.0 6.3 + - - +
599B GLU* 1.3 73.9 - - - +
601B PRO* 1.4 61.4 - - - +
602B LYS 3.2 2.1 + - - -
603B MET* 3.3 6.0 + - - +
604B LEU* 3.0 25.2 + - - +
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Residues in contact with PRO 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B GLU* 4.8 0.4 - - - -
600B LEU* 1.4 77.0 - - - +
602B LYS* 1.3 56.9 + - - +
604B LEU* 3.4 11.1 - - + +
605B ASP* 2.9 28.6 + - - +
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Residues in contact with LYS 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B GLU* 4.1 18.0 + - + +
600B LEU 3.2 0.8 - - - -
601B PRO* 1.3 77.2 - - - +
603B MET* 1.3 58.4 + - - +
605B ASP* 3.3 7.4 + - - +
606B GLY* 2.9 23.9 + - - -
648B TYR 4.8 1.2 - - - +
649B SER* 3.9 9.5 - - - -
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Residues in contact with MET 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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594B PRO* 5.0 13.7 - - + -
599B GLU 4.0 7.5 + - - +
600B LEU* 3.3 8.6 + - - +
602B LYS* 1.3 75.8 - - - +
604B LEU* 1.3 60.9 + - - +
606B GLY 3.8 0.2 - - - -
607B LEU* 2.9 30.1 + - - +
649B SER* 4.0 16.5 - - - -
651B ILE* 5.9 5.8 - - + -
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Residues in contact with LEU 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B LEU 3.0 14.4 + - - +
601B PRO* 3.4 14.6 - - + +
602B LYS 3.2 0.2 - - - -
603B MET* 1.3 76.8 - - - +
605B ASP* 1.3 58.3 + - - +
607B LEU* 3.3 5.7 + - - +
608B ARG* 2.9 28.4 + - - +
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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
----------------------------------------------------------
601B PRO 2.9 17.1 + - - +
602B LYS* 3.3 7.2 + - - +
604B LEU* 1.3 75.1 - - - +
606B GLY* 1.3 57.9 + - - +
608B ARG* 3.3 7.4 + - - +
609B LYS* 2.9 28.8 + - - +
648B TYR 5.3 0.2 - - - -
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Residues in contact with GLY 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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602B LYS 2.9 15.5 + - - -
603B MET 3.5 2.0 + - - -
605B ASP* 1.3 78.5 - - - +
607B LEU* 1.3 55.3 + - - +
609B LYS* 3.3 3.8 + - - +
610B VAL* 2.9 27.9 + - - +
644B LEU* 5.4 5.0 - - - -
648B TYR* 3.9 33.9 + - - +
649B SER* 4.1 7.2 - - - -
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Residues in contact with LEU 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 MET 2.9 19.9 + - - +
604B LEU* 3.7 6.3 - - - +
606B GLY* 1.3 73.0 - - - +
608B ARG* 1.3 61.2 + - - +
610B VAL* 3.3 7.8 + - - +
611B ASN* 2.9 28.6 + - - +
644B LEU* 6.0 2.5 - - - -
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Residues in contact with ARG 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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604B LEU 2.9 16.7 + - - +
605B ASP* 3.7 7.9 - - - +
606B GLY 3.3 0.2 - - - -
607B LEU* 1.3 75.6 - - - +
609B LYS* 1.3 57.3 + - - +
611B ASN* 3.3 8.0 + - - +
612B LYS* 2.9 28.1 + - - +
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Residues in contact with LYS 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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487B GLY 5.9 2.7 - - - +
605B ASP 2.9 17.2 + - - +
606B GLY* 3.3 8.3 + - - +
608B ARG* 1.3 73.9 - - - +
610B VAL* 1.3 59.7 + - - +
612B LYS* 3.4 8.7 + - - +
613B SER* 2.9 28.3 + - - -
648B TYR* 4.4 12.6 - - + -
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Residues in contact with VAL 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B GLY 2.9 16.9 + - - +
607B LEU* 3.6 9.2 - - - +
608B ARG 3.3 0.2 - - - -
609B LYS* 1.3 76.4 - - - +
611B ASN* 1.3 52.3 + - - +
613B SER* 3.0 6.7 + - - +
614B TYR* 2.6 42.8 + - + +
617B LEU* 5.7 1.1 - - - -
640B VAL* 5.1 10.5 - - + +
643B ASP* 5.9 2.5 - - + -
644B LEU* 4.9 17.5 - - + +
648B TYR* 5.3 1.7 - - + +
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Residues in contact with ASN 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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560B VAL* 3.9 18.6 - - + +
607B LEU 2.9 16.6 + - - +
608B ARG* 3.6 8.5 - - - +
610B VAL* 1.3 75.8 - - - +
612B LYS* 1.3 60.6 + - - +
614B TYR 3.0 22.3 - - - +
615B PRO* 4.3 1.9 - - - +
617B LEU* 4.9 13.2 - - + +
619B THR* 5.8 9.0 - - - +
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Residues in contact with LYS 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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481B MET* 3.8 25.8 + - + +
556B ASP 6.0 2.5 - - - +
559B ILE 5.0 10.5 - - - +
560B VAL* 4.4 13.4 - - - +
608B ARG 2.9 14.2 + - - +
609B LYS* 3.6 11.7 - - - +
610B VAL 3.2 0.2 - - - -
611B ASN* 1.3 78.4 - - - +
613B SER* 1.3 60.9 + - - +
614B TYR 3.5 1.6 + - - -
615B PRO* 4.9 2.1 - - - +
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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
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481B MET 4.1 16.1 - - - +
482B TYR 6.5 0.4 - - - -
609B LYS 2.9 17.9 + - - -
610B VAL* 3.0 7.1 + - - -
612B LYS* 1.3 77.0 - - - +
614B TYR* 1.3 57.4 + - - +
615B PRO 4.1 0.9 - - - -
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Residues in contact with TYR 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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610B VAL* 2.6 17.9 + - + +
611B ASN* 3.0 15.1 - - - +
612B LYS 3.3 0.6 - - - -
613B SER* 1.3 75.4 - - - +
615B PRO* 1.3 63.8 - - - +
616B SER 3.5 1.3 - - - -
617B LEU* 3.6 27.0 + - + +
640B VAL* 5.5 11.2 - - + -
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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