Contacts of the helix formed by residues 696 - 704 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B GLU* 3.4 24.4 + - - -
690B LEU* 3.1 23.5 + - - -
693B GLU* 3.4 23.0 + - - +
694B PRO 3.4 2.0 - - - -
695B GLU* 1.3 81.4 - - - +
697B LEU* 1.3 59.5 + - - +
699B SER* 3.2 13.7 + - - -
700B TYR* 3.0 26.4 + - - +
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Residues in contact with LEU 697 (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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502B GLY* 5.9 0.2 - - - -
503B ARG* 3.7 32.5 - - + +
675B VAL* 4.0 17.0 - - + -
676B MET 4.2 3.8 - - - +
677B GLU* 4.0 35.9 - - + +
682B VAL* 5.2 6.7 - - + -
683B GLU* 2.8 20.5 + - - +
695B GLU 4.0 1.0 + - - -
696B SER* 1.3 67.9 - - - +
698B TYR* 1.3 57.9 + - - +
700B TYR* 3.2 17.0 + - + +
701B LEU* 2.9 47.5 + - + +
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Residues in contact with TYR 698 (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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501B VAL* 4.3 2.9 - - + -
664B LEU* 3.6 38.1 + - + +
667B VAL* 5.2 0.6 - - + +
668B LYS* 5.0 0.7 - - - -
673B ILE* 3.4 38.3 - - + +
675B VAL* 3.8 25.7 - - + +
683B GLU* 2.8 16.0 + - - +
687B HIS* 2.7 49.3 + + - -
690B LEU* 3.6 33.4 - - + +
691B LEU* 4.3 9.2 - - + -
697B LEU* 1.3 77.6 - - - +
699B SER* 1.3 56.9 + - - +
701B LEU* 3.2 7.6 + - - +
702B TYR* 2.9 31.1 + - + +
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Residues in contact with SER 699 (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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690B LEU 4.2 3.6 - - - -
691B LEU* 4.0 23.1 + - - +
693B GLU 3.3 18.3 + - - -
694B PRO* 3.4 13.0 + - - +
696B SER* 3.2 23.7 + - - -
698B TYR* 1.3 79.0 - - - +
700B TYR* 1.3 61.9 + - - +
702B TYR* 3.5 1.4 + - - +
703B GLN* 3.2 24.3 + - - +
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Residues in contact with TYR 700 (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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639A GLU* 3.2 39.0 + - - +
503B ARG* 3.6 10.5 - - - -
694B PRO 5.2 0.6 + - - -
695B GLU* 6.0 1.1 - - - -
696B SER 3.0 12.7 + - - +
697B LEU* 3.2 26.9 + - + +
699B SER* 1.3 78.1 - - - +
701B LEU* 1.3 63.5 + - + +
703B GLN* 3.6 10.8 + - - +
704B LEU* 3.0 48.6 + - + +
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Residues in contact with LEU 701 (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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637A ASP* 6.0 5.6 - - + -
638A TYR* 4.4 15.6 - - + +
639A GLU* 4.4 9.4 - - + +
501B VAL* 5.4 2.0 - - + -
502B GLY* 4.8 18.4 - - - +
503B ARG* 5.0 13.7 - - + +
664B LEU* 4.3 26.2 - - + +
675B VAL* 5.2 4.5 - - + -
697B LEU* 2.9 38.1 + - + +
698B TYR* 3.2 6.7 + - - +
700B TYR* 1.3 94.3 - - + +
702B TYR* 1.3 57.9 + - - +
704B LEU* 2.8 40.7 - - + +
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Residues in contact with TYR 702 (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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706A SER 4.8 8.1 + - - -
707A ASP* 5.2 7.8 + - - -
664B LEU* 4.1 23.0 - - + +
665B SER* 5.8 8.7 - - - -
668B LYS* 5.5 7.3 - - + +
687B HIS* 4.0 27.7 + + - -
691B LEU* 3.5 36.0 - - + +
698B TYR* 2.9 17.9 + - + +
699B SER 4.0 1.8 - - - +
700B TYR 3.3 0.2 - - - -
701B LEU* 1.3 74.7 - - - +
703B GLN* 1.3 68.2 + - - +
704B LEU 3.4 5.7 - - - +
705B GLN 4.0 0.7 - - - +
706B SER* 3.3 40.3 + - - -
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Residues in contact with GLN 703 (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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699B SER 3.2 16.1 + - - +
700B TYR* 3.8 13.4 - - + +
702B TYR* 1.3 77.0 - - - +
704B LEU* 1.3 72.7 + - - +
705B GLN 3.0 5.2 + - - -
706B SER* 3.4 14.6 + - - -
707B ASP* 5.4 0.7 - - - +
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Residues in contact with LEU 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 3.9 22.1 - - + +
639A GLU* 3.9 21.8 - - + +
642A HIS* 5.6 3.6 - - + +
700B TYR* 3.0 53.4 + - + +
701B LEU* 2.8 37.2 - - + +
702B TYR 3.2 1.4 - - - +
703B GLN* 1.3 78.2 + - - +
705B GLN* 1.3 105.1 + - - +
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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