Contacts of the strand formed by residues 708 - 711 (chain A) in PDB entry 1QFG
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 708 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A TRP* 4.3 7.2 - - - -
703A CYS* 2.9 4.2 - - - +
704A PHE* 2.8 59.5 + - - -
705A ASN* 2.8 10.9 + - - +
706A THR 3.5 0.2 - - - -
707A TYR* 1.3 78.5 - - - +
709A CYS* 1.3 58.4 + - - -
710A PHE* 4.0 4.7 - - - -
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Residues in contact with CYS 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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243A TYR* 5.3 0.2 + - - -
245A GLY 4.7 0.2 - - - +
246A TRP 4.1 0.2 - - - -
247A LEU* 2.7 46.0 + - + +
249A LYS* 3.7 30.5 - - - -
252A THR* 3.8 16.8 - - - +
253A VAL* 4.1 0.7 - - - -
700A VAL* 4.3 3.4 - - + -
702A SER 3.5 2.7 - - - -
703A CYS* 2.0 44.6 - - - -
705A ASN 4.2 3.6 - - - -
708A GLY* 1.3 74.3 - - - -
710A PHE* 1.3 73.2 + - - +
711A TRP 4.3 0.2 - - - -
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Residues in contact with PHE 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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80A THR* 3.8 16.2 - - + +
81A ARG* 3.2 65.1 - - - +
243A TYR* 5.1 9.0 - + - -
245A GLY 3.1 26.0 - - - -
246A TRP* 3.8 14.8 - + - -
252A THR* 6.3 0.2 - - - -
619A GLN* 4.4 9.0 - - - -
700A VAL* 3.4 5.5 - - - +
701A ALA* 2.6 33.3 + - - +
702A SER* 2.9 21.5 + - - +
704A PHE* 4.0 25.1 - + - -
708A GLY 4.0 6.5 - - - -
709A CYS* 1.3 85.5 - - - +
711A TRP* 1.3 58.6 + - - +
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Residues in contact with TRP 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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81A ARG 4.6 0.2 - - - +
82A GLY* 3.6 1.0 - - - -
83A ALA* 3.3 20.1 + - - +
204A GLN* 4.0 2.7 - - - +
205A GLN* 5.6 4.7 - - - +
243A TYR* 6.3 0.4 - - - -
247A LEU* 3.8 30.7 - - + +
251A GLY 3.6 13.5 - - - -
252A THR* 3.6 26.2 - - + +
261A ARG* 4.5 7.4 - - + -
262A LEU 2.9 32.1 + - - -
263A PRO 3.3 8.5 + - - -
264A THR* 3.3 44.9 - - + +
266A PHE 5.1 2.0 - - - -
698A GLU* 4.1 19.3 - - + -
699A TYR* 3.1 34.5 - - - -
700A VAL* 3.2 22.0 - - + -
709A CYS 4.3 0.6 + - - -
710A PHE* 1.3 74.2 - - - +
712A GLY* 1.3 70.6 - - - +
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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