Contacts of the helix formed by residues 696 - 704 (chain D) in PDB entry 2FGJ
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 SER 696 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683D GLU* 3.3 22.2 - - - -
690D LEU* 2.9 17.5 + - - -
693D GLU* 2.7 42.1 + - - -
694D PRO 3.2 0.4 - - - -
695D GLU* 1.3 80.8 - - - +
697D LEU* 1.3 58.8 + - - +
698D TYR 4.0 0.3 + - - -
699D SER* 3.3 7.6 + - - -
700D TYR* 2.9 27.1 + - - +
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Residues in contact with LEU 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D ARG* 3.4 43.7 - - + +
675D VAL* 4.0 11.0 - - + -
676D MET 4.5 2.9 - - - +
677D GLU* 4.1 12.1 - - + -
682D VAL* 4.0 24.7 - - + -
683D GLU* 2.9 17.2 + - - +
695D GLU 3.8 1.4 + - - -
696D SER* 1.3 71.5 - - - +
698D TYR* 1.3 56.9 + - - +
700D TYR* 3.4 18.8 - - + +
701D LEU* 2.9 39.8 + - + +
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Residues in contact with TYR 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D VAL* 4.0 11.2 - - + -
664D LEU* 3.6 33.9 + - + +
667D VAL* 5.2 0.7 - - + +
668D LYS* 5.0 0.2 - - - -
673D ILE* 3.5 34.6 - - + +
675D VAL* 3.7 25.3 - - + +
683D GLU* 2.9 16.7 + - - +
687D HIS* 2.7 30.4 + + - -
690D LEU* 3.5 34.1 - - + -
691D LEU* 3.4 30.3 - - + -
696D SER* 4.3 2.2 - - - +
697D LEU* 1.3 76.2 - - - +
699D SER* 1.3 51.6 + - - +
701D LEU* 2.9 7.2 + - + +
702D TYR* 2.6 36.7 + - + +
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Residues in contact with SER 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690D LEU 3.3 9.2 + - - -
691D LEU* 3.5 18.3 + - - +
693D GLU 2.8 16.0 + - - -
694D PRO* 3.3 24.1 - - - +
696D SER* 3.2 13.8 + - - -
698D TYR* 1.3 79.4 - - - +
700D TYR* 1.3 57.0 + - - +
702D TYR* 3.9 8.7 - - - +
703D GLN* 2.9 30.3 + - - +
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Residues in contact with TYR 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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639C GLU* 3.4 18.6 + - - +
503D ARG* 3.7 19.5 - - - -
694D PRO 4.7 1.2 + - - -
695D GLU 5.6 1.8 - - - +
696D SER 2.9 13.1 + - - +
697D LEU* 3.4 23.3 - - + +
699D SER* 1.3 75.9 - - - +
701D LEU* 1.3 84.0 + - + +
703D GLN* 3.3 20.0 + - - +
704D LEU* 3.2 45.3 + - + +
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Residues in contact with LEU 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637C ASP* 5.6 5.2 - - + +
638C TYR* 3.2 32.7 - - + +
639C GLU* 5.0 12.6 - - + +
501D VAL* 5.3 1.8 - - + -
502D GLY* 4.5 26.9 - - - +
503D ARG* 5.0 9.9 - - + +
664D LEU* 3.9 21.3 - - + -
675D VAL* 4.7 8.5 - - + -
697D LEU* 2.9 37.1 + - + +
698D TYR* 3.6 4.7 - - - +
700D TYR* 1.3 101.1 - - + +
702D TYR* 1.3 61.4 + - - +
704D LEU* 3.3 14.7 + - + +
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Residues in contact with TYR 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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638C TYR* 5.4 1.4 - - - -
706C SER 4.5 0.3 + - - -
707C ASP* 3.3 40.8 - - - +
664D LEU* 3.6 24.4 - - + +
665D SER* 5.6 4.3 - - - -
668D LYS* 4.4 1.7 - - + -
687D HIS* 3.4 33.8 + + - -
691D LEU* 3.6 34.9 - - + +
698D TYR* 2.6 20.7 + - + +
699D SER* 3.9 8.7 - - - +
701D LEU* 1.3 71.2 - - - +
703D GLN* 1.3 62.9 + - - +
704D LEU 3.5 1.7 + - - +
706D SER* 2.9 40.6 + - - -
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Residues in contact with GLN 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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699D SER 2.9 18.6 + - - +
700D TYR* 3.3 27.0 + - - +
702D TYR* 1.3 79.0 - - - +
704D LEU* 1.3 73.4 + - - +
705D GLN 3.5 0.2 + - - -
706D SER* 3.6 9.1 + - - -
707D ASP* 3.0 39.4 + - - +
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Residues in contact with LEU 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C TYR* 3.3 29.3 - - + -
639C GLU* 4.0 25.1 - - + +
642C HIS* 4.2 24.9 - - + +
700D TYR* 3.2 54.7 + - + +
701D LEU* 3.3 14.8 - - + +
702D TYR 3.3 1.8 - - - +
703D GLN* 1.3 85.4 - - - +
705D GLN* 1.3 61.9 + - - +
706D SER 2.7 17.3 + - - -
707D ASP* 4.2 3.6 - - - +
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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