Contacts of the helix formed by residues 696 - 715 (chain r) 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 LYS 696 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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694r GLU* 3.5 7.4 - - + +
695r LYS* 1.3 79.4 - - - +
697r ALA* 1.3 62.8 + - - +
698r ILE* 4.4 7.2 - - + +
699r LYS* 3.7 13.3 + - + +
700r ARG* 3.4 19.1 + - - +
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Residues in contact with ALA 697 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695r LYS 3.3 6.7 + - - +
696r LYS* 1.3 71.2 - - - +
698r ILE* 1.3 60.6 + - - +
700r ARG* 3.1 10.2 + - + +
701r PHE* 2.9 32.2 + - - +
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Residues in contact with ILE 698 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696r LYS* 3.3 6.0 - - + -
697r ALA* 1.3 80.2 - - - +
699r LYS* 1.3 60.0 + - - +
701r PHE* 3.8 10.3 + - - +
702r GLN* 4.1 7.4 + - - +
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Residues in contact with LYS 699 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694r GLU* 5.2 8.5 - - + -
696r LYS* 3.7 16.4 + - + +
697r ALA 3.3 0.2 - - - -
698r ILE* 1.3 76.6 - - - +
700r ARG* 1.3 60.5 + - - +
701r PHE 3.2 0.7 - - - -
702r GLN* 3.1 10.0 + - - +
703r ILE* 3.0 26.2 + - - +
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Residues in contact with ARG 700 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692r ILE* 5.8 5.6 - - + -
694r GLU* 4.6 17.7 - - + +
696r LYS 3.4 13.9 + - - +
697r ALA* 3.1 15.2 + - + +
699r LYS* 1.3 74.6 - - - +
701r PHE* 1.3 55.4 + - - +
702r GLN 3.0 4.9 - - - -
703r ILE* 3.8 8.0 - - - +
704r MET* 2.9 35.2 + - - +
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Residues in contact with PHE 701 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697r ALA 2.9 15.1 + - - +
698r ILE* 4.2 7.6 - - - +
699r LYS 3.2 0.8 - - - -
700r ARG* 1.3 75.5 - - - +
702r GLN* 1.3 57.3 + - - +
704r MET* 4.7 3.6 - - - -
705r ASN* 4.1 11.8 + - - +
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Residues in contact with GLN 702 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698r ILE 4.1 5.0 + - - +
699r LYS* 3.1 13.3 + - - +
700r ARG 3.0 0.4 - - - -
701r PHE* 1.3 77.9 - - - +
703r ILE* 1.3 67.2 + - - +
704r MET 3.2 1.1 - - - -
705r ASN* 2.9 18.9 + - - +
706r GLU* 3.0 13.9 + - - +
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Residues in contact with ILE 703 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699r LYS 3.0 13.3 + - - +
700r ARG* 3.8 10.8 - - - +
702r GLN* 1.3 75.4 - - - +
704r MET* 1.3 56.2 + - - +
706r GLU* 3.2 9.0 + - - +
707r ILE* 2.9 27.6 + - - +
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Residues in contact with MET 704 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700r ARG 2.9 16.2 + - - +
701r PHE* 5.3 2.5 - - - -
703r ILE* 1.3 73.3 - - - +
705r ASN* 1.3 65.8 + - - +
707r ILE* 3.3 7.2 + - - +
708r VAL* 2.9 24.3 + - - +
870r ILE* 5.7 8.7 - - + -
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Residues in contact with ASN 705 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701r PHE 4.1 11.7 + - - +
702r GLN* 2.9 15.3 + - - +
704r MET* 1.3 77.0 - - - +
706r GLU* 1.3 58.1 + - - +
708r VAL* 3.1 10.0 - - - +
709r TYR* 2.9 25.9 + - - +
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Residues in contact with GLU 706 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702r GLN 3.0 11.4 + - - +
703r ILE* 3.2 10.3 + - - +
705r ASN* 1.3 74.3 - - - +
707r ILE* 1.3 60.9 + - - +
709r TYR* 3.2 7.7 + - - +
710r GLU* 2.9 30.0 + - - +
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Residues in contact with ILE 707 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690r VAL* 5.9 7.2 - - + -
703r ILE 2.9 13.1 + - - +
704r MET* 3.7 11.2 - - - +
706r GLU* 1.3 72.9 - - - +
708r VAL* 1.3 66.0 + - - +
710r GLU* 3.4 4.5 + - - +
711r LYS* 2.9 28.6 + - - +
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Residues in contact with VAL 708 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704r MET 2.9 13.2 + - - +
705r ASN* 3.1 13.7 - - - +
707r ILE* 1.3 76.9 - - - +
709r TYR* 1.3 57.1 + - - +
711r LYS* 3.8 4.7 - - - +
712r ILE* 2.9 33.5 + - - +
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Residues in contact with TYR 709 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705r ASN 2.9 13.0 + - - +
706r GLU* 3.2 11.6 + - - +
708r VAL* 1.3 76.1 - - - +
710r GLU* 1.3 58.0 + - - +
712r ILE* 3.2 4.4 + - - +
713r MET* 2.9 30.9 + - - +
741r MET* 5.8 8.7 - - + -
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Residues in contact with GLU 710 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706r GLU 2.9 15.6 + - - +
707r ILE* 4.1 4.0 - - - +
709r TYR* 1.3 77.1 - - - +
711r LYS* 1.3 58.1 + - - +
713r MET* 3.3 5.4 + - - +
714r GLU* 3.0 28.6 + - - +
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Residues in contact with LYS 711 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707r ILE 2.9 20.4 + - - +
708r VAL* 3.8 4.5 - - - +
710r GLU* 1.3 76.7 - - - +
712r ILE* 1.3 62.0 + - - +
714r GLU* 3.3 19.6 + - - +
715r HIS* 3.6 7.8 + - - +
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Residues in contact with ILE 712 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708r VAL 2.9 18.9 + - - +
709r TYR* 3.8 4.5 - - - +
711r LYS* 1.3 76.3 - - - +
713r MET* 1.3 59.5 + - - +
714r GLU 3.2 0.4 - - - -
715r HIS* 3.2 7.6 + - - +
716r ALA* 3.1 24.0 + - - +
721r VAL* 5.6 11.2 - - + -
738r ILE* 6.4 1.6 - - + -
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Residues in contact with MET 713 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709r TYR 2.9 17.7 + - - +
710r GLU* 3.9 5.8 - - - +
712r ILE* 1.3 74.2 - - - +
714r GLU* 1.3 66.4 + - - +
716r ALA* 3.2 23.9 + - + +
717r GLY 4.8 0.3 + - - -
749r GLY* 6.5 1.3 - - - -
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Residues in contact with GLU 714 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710r GLU 3.0 14.2 + - - +
711r LYS* 3.3 15.7 - - - +
712r ILE 3.2 0.2 - - - -
713r MET* 1.3 79.2 - - - +
715r HIS* 1.3 58.6 + - + +
716r ALA 3.7 0.2 + - - -
717r GLY 4.7 1.7 + - - -
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Residues in contact with HIS 715 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711r LYS 3.6 7.3 + - - +
712r ILE* 3.2 8.7 + - - +
713r MET 3.2 0.4 - - - -
714r GLU* 1.3 76.8 - - + +
716r ALA* 1.3 56.9 + - - +
717r GLY 2.9 21.2 + - - +
719r ASN* 3.5 29.4 - - + +
720r GLN 5.4 3.4 - - - +
721r VAL* 5.1 15.3 - - + -
807r GLN* 6.1 0.2 - - - +
825r THR* 5.6 8.5 - - - -
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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
------------------------------------------------------------
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