Contacts of the helix formed by residues 705 - 716 (chain A) in PDB entry 3FVO
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 ASN 705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A LEU 6.1 1.1 - - - +
426A GLU* 6.0 0.7 - - - +
472A GLY 5.7 2.0 - - - +
670A VAL* 3.7 13.7 - - - -
703A VAL* 3.4 7.4 - - - +
704A ARG* 1.3 94.0 - - + +
706A SER* 1.3 65.0 + - - +
707A ASP* 3.3 11.3 + - - +
708A GLU* 2.9 36.2 + - - +
709A GLY 3.1 16.6 + - - -
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Residues in contact with SER 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 8EP 3.8 23.5 - - - -
426A GLU* 2.5 34.6 + - - -
670A VAL* 3.7 10.6 - - - +
705A ASN* 1.3 74.6 - - - +
707A ASP* 1.3 57.9 + - - +
709A GLY* 3.1 2.8 + - - +
710A ILE* 2.8 33.1 + - - +
720A LEU* 4.3 3.2 - - - +
722A MET* 4.2 5.2 - - - -
969A GOL 2.8 21.4 + - - -
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Residues in contact with ASP 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU* 4.5 14.5 - - - +
705A ASN* 3.3 10.7 + - - +
706A SER* 1.3 81.6 + - - +
708A GLU* 1.3 57.2 + - - +
710A ILE* 3.4 9.2 + - - +
711A GLN* 2.9 35.6 + - + +
969A GOL 3.8 13.8 + - - -
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Residues in contact with GLU 708 (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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702A LEU 4.9 0.2 - - - +
703A VAL* 3.4 15.6 - - + +
704A ARG* 2.9 55.4 + - - +
705A ASN* 2.9 23.5 + - - +
707A ASP* 1.3 75.0 - - - +
709A GLY* 1.3 63.9 + - - +
711A GLN* 3.4 8.1 + - + +
712A ARG* 3.0 26.7 + - + +
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Residues in contact with GLY 709 (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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703A VAL* 3.8 25.5 - - - +
705A ASN 3.1 10.7 + - - -
706A SER 3.1 4.2 + - - -
708A GLU* 1.3 76.9 - - - +
710A ILE* 1.3 56.0 + - - +
712A ARG* 3.2 5.7 + - - +
713A VAL* 3.0 30.0 + - - +
718A TYR* 4.1 1.5 - - - -
720A LEU* 4.0 18.6 - - - -
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Residues in contact with ILE 710 (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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526A LEU* 3.9 18.8 - - + -
706A SER 2.8 20.8 + - - +
707A ASP* 3.9 10.1 - - - +
709A GLY* 1.3 70.9 - - - +
711A GLN* 1.3 65.9 + - + +
713A VAL* 3.2 8.3 + - - +
714A LEU* 2.9 41.8 + - + +
720A LEU* 4.6 0.2 - - + -
722A MET* 4.0 8.5 - - + -
730A VAL* 3.8 14.8 - - + -
734A ASN* 5.6 0.4 - - - +
737A LEU* 4.1 17.0 - - + -
969A GOL 3.4 36.1 - - - +
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Residues in contact with GLN 711 (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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707A ASP* 2.9 23.5 + - + +
708A GLU* 3.6 8.1 - - + +
710A ILE* 1.3 75.7 - - + +
712A ARG* 1.3 58.2 + - - +
714A LEU* 3.2 15.2 + - - +
715A THR* 2.8 51.8 + - - +
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Residues in contact with ARG 712 (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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666A GLU* 2.8 19.3 + - - -
700A THR* 2.3 61.3 + - - +
703A VAL* 4.0 12.1 - - - +
708A GLU* 3.0 16.0 + - + +
709A GLY 3.3 9.6 - - - +
711A GLN* 1.3 74.9 - - - +
713A VAL* 1.3 59.4 + - - +
715A THR* 4.0 4.3 - - - -
716A THR* 2.7 55.0 + - + +
718A TYR* 3.3 36.6 - - + +
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Residues in contact with VAL 713 (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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526A LEU* 4.0 9.0 - - + +
527A TYR* 3.8 26.2 - - + +
528A ARG* 2.6 33.1 + - + +
709A GLY 3.0 20.7 + - - +
710A ILE* 3.5 8.3 - - - +
712A ARG* 1.3 75.3 - - - +
714A LEU* 1.3 54.0 + - - +
716A THR 3.2 6.9 - - - +
718A TYR* 3.3 24.1 - - + +
720A LEU* 3.8 29.4 - - + +
737A LEU* 3.7 25.6 - - + -
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Residues in contact with LEU 714 (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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528A ARG* 3.6 20.7 + - + +
710A ILE* 2.9 34.5 + - + +
711A GLN* 3.2 17.2 + - - +
713A VAL* 1.3 78.2 - - - +
715A THR* 1.3 63.1 + - + +
734A ASN* 3.7 26.7 - - - +
736A ASN* 4.4 15.0 - - + +
737A LEU* 3.7 26.5 - - + -
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Residues in contact with THR 715 (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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528A ARG* 5.0 1.3 - - - -
711A GLN* 2.8 36.6 + - - +
712A ARG* 4.0 1.7 - - - -
714A LEU* 1.3 85.5 - - + +
716A THR* 1.3 73.5 + - - +
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Residues in contact with THR 716 (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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528A ARG* 2.5 26.2 + - - -
666A GLU* 5.3 0.7 + - - -
712A ARG* 2.7 45.9 + - + +
713A VAL 3.2 2.3 - - - +
715A THR* 1.3 91.0 - - - +
717A ASP* 1.3 57.0 + - - +
718A TYR* 3.0 13.5 + - - +
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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