Contacts of the helix formed by residues 696 - 707 (chain D) in PDB entry 6M17
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 PRO 696 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616D GLN* 3.4 15.5 - - - +
694D ILE 3.7 6.5 - - - +
695D ILE* 1.3 98.1 - - + +
697D ARG* 1.3 66.3 + - - +
698D THR* 3.2 15.3 - - + +
699D GLU* 3.3 20.1 + - + +
700D VAL* 3.3 15.8 + - - +
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Residues in contact with ARG 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D ASP 4.3 12.9 + - - +
616D GLN* 3.6 31.8 + - - +
617D SER 3.2 23.5 + - - -
618D ILE* 4.0 26.0 - - + +
619D LYS 4.7 1.8 - - - +
695D ILE 3.8 0.4 + - - -
696D PRO* 1.3 74.2 - - - +
698D THR* 1.3 65.1 + - + +
700D VAL* 3.5 6.1 + - - +
701D GLU* 2.4 66.6 + - - +
725D LEU 3.5 23.8 + - - -
726D GLY* 4.6 6.3 - - - -
727D ILE* 5.5 0.2 - - - +
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Residues in contact with THR 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696D PRO* 4.2 8.3 - - + +
697D ARG* 1.3 82.1 - - + +
699D GLU* 1.3 71.4 + - - +
701D GLU* 3.8 14.7 + - - +
702D LYS* 3.3 41.8 + - - +
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Residues in contact with GLU 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651D MET* 4.7 1.8 - - - +
654D TYR* 3.2 40.9 + - + -
655D PHE* 5.4 7.1 - - + -
659D LYS* 3.8 19.3 + - - -
695D ILE* 4.1 15.0 - - + -
696D PRO* 3.3 22.9 + - + +
697D ARG 3.3 0.2 - - - -
698D THR* 1.3 86.6 + - - +
700D VAL* 1.3 62.0 + - - +
701D GLU 3.4 0.2 - - - -
702D LYS* 3.7 11.6 + - - +
703D ALA* 3.3 23.7 + - - +
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Residues in contact with VAL 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D GLN 6.0 1.6 - - - +
618D ILE* 3.8 21.3 - - + -
647D VAL* 5.5 0.9 - - + -
651D MET* 4.2 11.4 - - + -
683D PHE* 4.2 5.8 - - + -
684D PHE* 6.4 0.4 - - - -
685D VAL* 4.0 31.2 - - + +
695D ILE* 4.0 20.2 - - + +
696D PRO 3.3 18.7 + - - +
697D ARG* 3.5 5.8 + - - +
698D THR 3.4 0.2 - - - -
699D GLU* 1.3 75.7 - - - +
701D GLU* 1.3 61.8 + - - +
702D LYS 3.3 0.2 - - - -
703D ALA* 3.3 5.3 + - - +
704D ILE* 2.9 40.3 + - + +
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Residues in contact with GLU 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D ILE* 4.3 6.1 - - + -
697D ARG* 2.4 55.7 + - - +
698D THR* 3.8 17.2 - - - +
700D VAL* 1.3 78.3 - - - +
702D LYS* 1.3 58.7 + - + +
704D ILE* 4.0 0.9 - - - +
705D ARG* 3.1 40.2 + - - +
726D GLY 4.1 10.2 - - - +
727D ILE* 3.7 32.2 - - + +
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Residues in contact with LYS 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654D TYR* 3.4 38.0 - - + +
698D THR* 3.3 30.6 + - - +
699D GLU* 3.7 13.0 + - - +
700D VAL 3.3 0.4 - - - -
701D GLU* 1.3 81.5 + - + +
703D ALA* 1.3 62.0 + - - +
705D ARG* 3.8 9.6 + - - +
706D MET* 3.4 21.3 + - - +
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Residues in contact with ALA 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650D ALA* 3.9 21.1 - - + +
651D MET* 3.7 26.2 - - - -
654D TYR* 3.7 28.5 - - + -
699D GLU 3.3 17.2 + - - +
700D VAL 3.3 4.1 + - - +
702D LYS* 1.3 76.1 - - - +
704D ILE* 1.3 64.2 + - + +
706D MET* 3.5 9.4 + - - +
707D SER* 3.5 9.2 + - - -
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Residues in contact with ILE 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D ILE* 4.5 5.6 - - + -
647D VAL* 5.3 7.6 - - + -
650D ALA* 5.1 6.7 - - + -
651D MET* 6.1 0.9 - - - -
683D PHE* 3.6 31.4 - - + -
700D VAL* 2.9 28.9 + - + +
701D GLU 4.1 2.7 - - - +
703D ALA* 1.3 75.4 - - + +
705D ARG* 1.3 61.2 + - - +
707D SER 3.2 2.0 + - - +
708D ARG* 2.9 37.1 + - + +
711D ILE* 4.9 12.1 - - + -
724D PHE* 3.8 44.9 - - + -
727D ILE* 4.1 14.6 - - + -
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Residues in contact with ARG 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701D GLU* 3.1 25.0 + - - +
702D LYS* 4.0 9.9 - - - +
704D ILE* 1.3 78.5 - - - +
706D MET* 1.3 59.6 + - - +
708D ARG* 4.0 13.5 + - - +
726D GLY 4.7 2.6 + - - -
727D ILE* 3.6 26.7 - - + +
728D GLN* 3.0 44.9 + - - +
729D PRO* 5.2 0.2 - - - +
730D THR* 3.5 19.8 + - - +
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Residues in contact with MET 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650D ALA 5.7 0.4 - - - +
653D GLN* 3.7 34.1 - - + +
654D TYR* 4.1 25.6 - - + -
657D LYS* 3.9 22.0 - - + -
658D VAL* 4.4 10.8 - - - -
702D LYS 3.4 15.1 + - - +
703D ALA* 3.7 7.2 - - - +
704D ILE 3.2 1.0 - - - -
705D ARG* 1.3 80.0 - - - +
707D SER* 1.3 67.9 + - - +
708D ARG 3.7 0.6 + - - -
709D SER 5.5 0.2 + - - -
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Residues in contact with SER 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649D TYR* 4.7 8.1 + - - -
650D ALA* 3.9 32.5 + - - +
653D GLN* 4.6 6.2 - - - +
703D ALA 3.5 3.1 + - - -
704D ILE 3.2 5.5 + - - -
706D MET* 1.3 94.1 + - - +
708D ARG* 1.3 62.7 + - - +
709D SER 3.3 2.7 - - - +
710D ARG* 3.3 15.6 + - - +
711D ILE* 3.2 26.5 + - - +
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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
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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