Contacts of the strand formed by residues 704 - 708 (chain C) in PDB entry 4GZZ
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 HIS 704 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569C VAL* 4.4 12.8 - - + +
634C GLY* 3.2 22.3 + - - +
635C THR* 4.6 17.3 - - + -
702C SER* 3.0 32.0 + - - -
703C ILE* 1.3 74.0 - - - +
705C ILE* 1.3 62.1 + - - +
706C GLU* 4.0 1.6 - - + +
827C VAL 3.9 0.9 - - - +
828C ALA* 3.2 2.1 - - - -
829C GLN* 2.9 38.5 + - + +
831C ARG* 3.7 46.0 + - + +
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Residues in contact with ILE 705 (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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628C PHE* 4.6 16.6 - - + +
629C TYR 4.6 0.2 - - - -
630C ARG* 2.5 71.9 + - + +
634C GLY* 3.3 8.0 + - - +
635C THR 4.8 1.1 - - - +
636C ALA* 4.5 14.1 - - + -
703C ILE* 4.3 7.2 - - + +
704C HIS* 1.3 78.8 - - - +
706C GLU* 1.3 56.1 + - - +
801C VAL* 4.6 6.1 - - + -
802C ARG* 6.2 1.6 - - - +
826C TYR* 3.8 40.8 - - + -
827C VAL 3.5 10.3 - - - +
828C ALA* 4.0 14.6 - - + +
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Residues in contact with GLU 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630C ARG* 4.6 5.8 + - - +
704C HIS* 4.0 2.4 + - + +
705C ILE* 1.3 71.2 - - - +
707C ARG* 1.3 66.0 + - - +
708C TYR* 3.5 44.9 + - + +
796C GLU 5.7 2.0 - - - +
797C GLY 6.2 0.2 - - - +
825C VAL 3.7 0.2 - - - +
827C VAL* 3.0 28.7 + - + +
829C GLN* 6.0 2.9 - - + +
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Residues in contact with ARG 707 (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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630C ARG* 4.1 33.6 - - - +
705C ILE 3.5 3.6 + - - -
706C GLU* 1.3 74.4 - - - +
708C TYR* 1.3 71.4 + - - +
709C GLU* 3.2 31.8 + - - +
824C ARG* 3.4 45.8 - - + +
825C VAL 3.3 9.6 - - - +
826C TYR* 4.0 17.7 - - + +
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Residues in contact with TYR 708 (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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706C GLU* 3.7 40.9 + - + +
707C ARG* 1.3 77.5 - - - +
709C GLU* 1.3 66.1 + - - +
755C LEU* 3.8 25.1 - - + -
790C LEU* 4.3 11.0 - - + -
791C ARG 5.5 0.4 - - - -
792C VAL* 4.8 7.6 - - + -
793C PRO* 3.4 43.5 - - + +
795C GLY* 5.9 0.2 - - - -
796C GLU 3.2 24.9 + - - -
797C GLY* 5.2 0.2 - - - -
823C VAL 4.6 0.2 - - - -
824C ARG* 3.3 6.2 - - - +
825C VAL* 3.0 30.4 + - - +
827C VAL* 4.0 24.9 - - + -
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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