Contacts of the helix formed by residues 696 - 704 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683C GLU* 3.1 21.4 + - - -
690C LEU 3.3 9.9 + - - -
693C GLU* 3.7 23.2 + - - +
694C PRO 3.6 2.8 + - - -
695C GLU* 1.3 80.9 - - - +
697C LEU* 1.3 63.3 + - - +
698C TYR 3.6 2.3 + - - -
699C SER* 2.9 27.7 + - - -
700C TYR* 3.2 22.7 + - - +
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Residues in contact with LEU 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C GLY* 5.9 0.7 - - - -
503C ARG* 3.3 42.2 - - + +
675C VAL* 3.7 24.9 - - + -
676C MET 4.1 2.9 - - - +
677C GLU* 3.8 28.5 - - + +
682C VAL* 3.8 8.5 - - + -
683C GLU* 3.1 16.1 + - - +
696C SER* 1.3 69.2 - - - +
698C TYR* 1.3 64.8 + - - +
700C TYR* 3.5 7.7 + - + +
701C LEU* 3.2 35.4 + - + +
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Residues in contact with TYR 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C VAL* 4.4 4.9 - - + -
664C LEU* 3.7 37.5 + - + +
667C VAL* 5.7 0.7 - - + -
668C LYS* 5.1 0.9 - - - -
673C ILE* 3.7 34.5 - - + +
675C VAL* 3.9 22.8 - - + +
683C GLU* 3.2 16.8 + - - +
687C HIS* 2.9 39.7 + + - -
690C LEU* 3.6 36.6 - - + -
691C LEU* 4.2 7.0 - - + -
696C SER* 3.3 3.1 - - - +
697C LEU* 1.3 77.8 - - - +
699C SER* 1.3 57.5 + - - +
701C LEU* 3.3 7.1 + - + +
702C TYR* 2.9 35.7 + + + +
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Residues in contact with SER 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690C LEU 3.3 10.0 + - - -
691C LEU* 3.6 25.0 + - - +
693C GLU 2.6 29.2 + - - -
694C PRO 3.7 13.2 - - - -
696C SER* 2.9 20.2 + - - -
697C LEU 3.3 0.2 - - - -
698C TYR* 1.3 73.8 - - - +
700C TYR* 1.3 60.5 + - - +
702C TYR* 4.5 0.3 - - - +
703C GLN* 3.1 28.1 + - - +
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Residues in contact with TYR 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ARG* 4.1 17.3 - - - -
695C GLU 6.0 0.2 - - - -
696C SER 3.2 16.2 + - - +
697C LEU* 3.7 7.6 - - + +
699C SER* 1.3 76.6 - - - +
701C LEU* 1.3 68.0 + - + +
703C GLN* 3.5 10.0 + - + +
704C LEU* 3.0 45.2 + - + +
639D GLU* 3.1 34.8 + - - +
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Residues in contact with LEU 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C VAL* 5.2 4.7 - - + -
502C GLY* 4.9 18.4 - - - -
503C ARG* 5.1 16.2 - - + +
664C LEU* 3.9 24.5 - - + -
675C VAL* 5.0 5.2 - - + -
697C LEU* 3.2 37.7 + - + +
698C TYR* 3.3 6.5 + - - +
700C TYR* 1.3 84.8 - - + +
702C TYR* 1.3 54.3 + - - +
704C LEU* 2.7 32.3 + - + +
637D ASP* 5.2 4.7 - - + +
638D TYR* 3.3 34.6 - - + +
639D GLU* 5.0 10.8 - - + +
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Residues in contact with TYR 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664C LEU* 3.7 27.5 - - + +
665C SER* 5.4 12.6 - - - -
668C LYS* 4.3 16.7 + - + -
687C HIS* 3.7 26.8 + + - -
691C LEU* 3.7 37.2 - - + -
698C TYR* 2.9 21.6 + - + +
701C LEU* 1.3 73.4 - - - +
703C GLN* 1.3 66.8 + - - +
704C LEU 3.1 8.5 - - - +
705C GLN 4.3 1.9 - - - +
706C SER* 3.1 19.4 + - - -
638D TYR* 5.3 0.7 - - - -
706D SER 5.3 2.6 + - - -
707D ASP* 4.4 11.1 + - - -
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Residues in contact with GLN 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691C LEU* 5.3 0.2 - - - +
699C SER 3.1 21.0 + - - +
700C TYR* 3.5 13.1 - - + +
701C LEU 3.3 0.2 - - - -
702C TYR* 1.3 77.5 - - - +
704C LEU* 1.3 63.5 + - - +
705C GLN 3.5 1.6 + - - -
706C SER* 3.0 20.7 + - - +
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Residues in contact with LEU 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700C TYR* 3.0 37.6 + - + +
701C LEU* 2.7 30.2 - - + +
702C TYR* 3.1 5.7 - - - +
703C GLN* 1.3 80.7 + - - +
705C GLN* 1.3 92.0 + - + +
638D TYR* 3.9 35.2 - - + +
639D GLU* 4.2 19.7 - - + +
642D HIS* 4.8 20.4 - - + +
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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