Contacts of the strand formed by residues 766 - 773 (chain A) in PDB entry 5C58
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 ARG 766 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 2.6 31.1 + - - +
144A GLU* 3.4 36.5 - - - +
146A THR 4.1 5.5 + - - -
149A ALA 2.3 30.5 + - - -
150A TYR* 3.6 38.6 + - + +
151A SER 5.6 0.4 - - - +
705A TYR* 4.1 6.0 - - - -
706A THR* 3.1 33.9 + - + +
764A GLY 3.4 2.6 + - - +
765A ASP* 1.3 76.6 - - - +
767A GLY* 1.3 61.9 + - - +
788A PHE 3.6 5.8 - - - +
789A ALA* 3.6 15.9 - - + +
790A PRO* 4.6 1.1 - - - -
810A TYR* 4.7 11.6 + - - +
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Residues in contact with GLY 767 (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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144A GLU 4.9 3.5 - - - +
704A THR* 3.1 19.1 - - - -
705A TYR* 4.0 9.2 - - - -
766A ARG* 1.3 79.1 - - - +
768A SER* 1.3 63.3 + - - -
787A ARG* 3.9 3.3 - - - +
788A PHE* 2.9 36.1 + - - +
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Residues in contact with SER 768 (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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144A GLU 4.2 14.8 - - - -
145A GLN* 3.8 20.4 - - - +
702A ASP* 4.2 4.2 + - - -
703A LEU* 3.3 5.0 - - - +
704A THR* 2.6 52.9 + - - +
767A GLY* 1.3 76.3 - - - -
769A VAL* 1.3 64.7 + - - +
770A THR* 5.1 0.7 - - - +
785A THR* 4.8 4.7 - - - -
786A VAL 3.2 13.5 - - - -
787A ARG* 4.6 6.1 - - - -
788A PHE* 4.0 5.2 - - - -
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Residues in contact with VAL 769 (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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701A ALA* 6.0 1.6 - - + -
702A ASP 3.2 7.9 - - - +
703A LEU* 4.5 18.8 - - + -
768A SER* 1.3 78.3 - - - +
770A THR* 1.3 64.7 + - - +
771A LEU* 4.2 23.7 + - + +
784A VAL 3.5 2.4 - - - +
786A VAL* 2.9 50.3 + - + +
788A PHE* 4.3 14.1 - - + -
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Residues in contact with THR 770 (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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145A GLN* 3.4 25.1 - - + +
700A TYR* 3.6 11.3 - - - +
701A ALA* 3.2 9.4 - - - +
702A ASP* 2.8 47.8 + - + +
768A SER* 5.1 0.4 - - - +
769A VAL* 1.3 79.0 - - - +
771A LEU* 1.3 64.0 + - - +
772A GLY 3.9 0.2 - - - -
784A VAL 3.2 5.8 - - - -
785A THR* 3.2 32.5 - - + +
816A TYR* 4.6 9.6 - - - -
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Residues in contact with LEU 771 (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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699A PHE* 4.1 28.3 - - + -
700A TYR 3.7 2.2 - - - -
701A ALA* 4.2 8.5 - - + -
769A VAL* 4.4 17.7 - - + +
770A THR* 1.3 78.8 - - - +
772A GLY* 1.3 59.1 + - - +
782A ALA 4.4 0.2 - - - +
783A GLY* 3.2 3.2 - - - -
784A VAL* 3.0 43.5 + - + +
786A VAL* 6.5 0.9 - - + -
816A TYR* 5.0 0.2 - - - -
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Residues in contact with GLY 772 (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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699A PHE* 3.3 10.6 - - - -
700A TYR* 2.8 56.4 + - - -
770A THR 3.9 1.6 - - - -
771A LEU* 1.3 74.7 - - - +
773A GLY* 1.3 58.1 + - - -
782A ALA 3.3 9.6 - - - -
783A GLY* 3.6 4.5 - - - -
816A TYR* 4.2 0.4 + - - -
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Residues in contact with GLY 773 (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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698A VAL 3.3 13.9 - - - -
699A PHE* 4.2 1.1 - - - -
700A TYR* 3.6 3.4 - - - -
772A GLY* 1.3 74.0 - - - -
774A ARG* 1.3 65.1 + - - -
780A LEU 3.1 2.6 - - - +
781A ASP* 3.5 4.2 - - - +
782A ALA* 2.8 37.7 + - - +
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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