Contacts of the helix formed by residues 696 - 702 (chain A) in PDB entry 1FGR
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 GLY 696 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A VAL* 3.6 13.0 - - - +
692A ALA 5.0 0.8 + - - -
694A ASN 3.0 2.4 + - - +
695A PHE* 1.3 76.4 - - - +
697A GLU* 1.3 65.4 + - - +
699A PRO* 3.5 5.2 - - - -
700A TYR* 3.0 30.5 + - - +
819A LEU* 3.6 12.2 - - - +
830A PHE* 3.9 23.6 - - - -
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Residues in contact with GLU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A VAL* 3.7 18.3 - - + +
494A HIS* 3.1 17.0 - - + -
495A GLN* 3.3 11.9 + - - -
499A HIS* 3.0 32.4 + - - -
694A ASN* 3.1 23.3 + - - +
695A PHE 3.3 1.2 - - - -
696A GLY* 1.3 76.2 - - - +
698A TYR* 1.3 60.2 + - - +
701A GLY* 2.7 30.1 + - - -
751A ILE* 3.4 27.1 - - + +
754A LEU* 3.3 25.8 - - + +
755A SER* 3.4 9.2 - - - +
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Residues in contact with TYR 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TYR* 5.1 0.5 - - - +
327A PHE* 3.4 21.7 - + - +
328A PRO* 2.6 43.9 + - + +
329A GLN 4.5 0.7 - - - -
330A PRO* 3.7 23.9 - - + +
331A HIS* 6.1 0.2 - - - -
697A GLU* 1.3 71.2 - - - +
699A PRO* 1.3 71.4 - - + +
700A TYR 3.2 0.2 - - - -
702A GLY* 2.8 40.8 + - - -
748A LEU* 3.7 34.6 - - + +
751A ILE* 3.7 17.2 + - + +
752A GLU* 3.7 20.0 - - + -
755A SER* 2.8 23.7 + - - +
828A LEU* 3.8 17.7 - - + -
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Residues in contact with PRO 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A PRO* 3.9 0.3 - - - +
331A HIS* 3.5 28.3 + - + +
332A VAL* 2.9 32.9 + - - +
695A PHE 3.4 19.3 - - - +
696A GLY 3.5 9.4 - - - +
698A TYR* 1.3 97.0 - - + +
700A TYR* 1.3 57.8 + - - +
755A SER* 3.8 3.1 - - - +
815A LEU* 5.1 0.7 - - + -
828A LEU* 3.7 21.1 - - + -
830A PHE* 3.4 33.0 - - + -
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Residues in contact with TYR 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A VAL* 3.8 17.8 - - + +
345A GLU* 3.9 1.1 - - - -
348A ARG* 3.2 26.4 + - - -
349A GLU* 3.3 35.7 - - - +
352A ALA 2.7 20.3 + - - -
353A GLY* 3.5 18.8 - - - -
354A VAL* 3.7 19.5 - - + -
696A GLY* 3.0 21.2 + - - +
699A PRO* 1.3 75.2 - - - +
701A GLY* 1.3 62.4 + - - +
702A GLY 3.4 2.4 + - - -
703A LEU 4.1 0.7 + - - +
706A ASN* 2.9 32.8 + - - +
707A ARG* 3.6 8.0 - - + +
813A VAL* 5.1 0.2 - - + -
815A LEU* 3.9 14.5 + - + +
817A TYR* 4.7 1.4 - - - -
819A LEU* 4.6 1.8 - - + -
830A PHE* 3.5 35.1 - + - -
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Residues in contact with GLY 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A GLU 2.7 19.8 + - - -
700A TYR* 1.3 72.9 - - - +
702A GLY* 1.3 61.8 + - - +
703A LEU 3.0 15.2 + - - +
704A ILE* 4.0 4.9 + - - +
707A ARG* 3.5 26.8 - - - +
748A LEU* 3.7 5.9 - - - +
751A ILE* 3.5 18.5 - - - +
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Residues in contact with GLY 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A VAL* 5.7 1.2 - - - +
293A TYR* 5.2 3.8 - - - -
330A PRO* 3.5 21.8 - - - +
698A TYR* 2.8 36.4 + - - -
700A TYR 3.4 1.0 - - - -
701A GLY* 1.3 76.5 - - - +
703A LEU* 1.3 56.8 + - - +
704A ILE 3.9 0.7 + - - -
748A LEU* 3.3 27.8 - - - +
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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