Contacts of the strand formed by residues 748 - 755 (chain A) in PDB entry 3FCS
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 VAL 748 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746A ALA 4.1 0.4 - - - -
747A GLN* 1.3 73.2 - - - +
749A GLU* 1.3 62.6 + - - +
786A LEU* 3.6 22.2 - - + -
787A HIS 3.4 14.4 - - - +
788A ASN* 4.4 11.2 - - + +
794A VAL* 4.4 17.3 - - + -
797A LEU* 4.3 9.2 - - + -
895A MET* 5.5 0.4 - - - -
930A PHE* 3.5 40.3 - - + -
932A VAL* 4.4 8.7 - - + -
945A PRO* 3.8 25.7 - - + +
946A ARG 5.0 1.4 - - - +
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Residues in contact with GLU 749 (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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747A GLN 3.9 1.1 + - - +
748A VAL* 1.3 74.1 - - - +
750A LEU* 1.3 65.2 + - - +
751A ARG* 3.7 39.4 + - + +
785A GLU 3.5 1.4 - - - +
786A LEU* 3.3 8.1 - - - +
787A HIS* 2.9 51.0 + - + +
789A ASN* 6.1 1.3 - - + -
591B PRO* 5.8 0.3 - - - +
592B GLY 6.1 0.9 - - - -
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Residues in contact with LEU 750 (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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748A VAL 4.3 0.8 + - - -
749A GLU* 1.3 76.3 - - - +
751A ARG* 1.3 67.6 + - - +
784A TYR* 4.3 13.7 - - + -
785A GLU 3.3 17.3 - - - +
786A LEU* 3.4 25.4 - - + -
799A LEU* 4.2 13.7 - - + -
928A ALA* 3.8 27.6 - - + +
930A PHE* 3.9 27.2 - - + -
948A GLU 4.1 6.5 - - - +
949A ALA* 3.6 34.8 - - + +
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Residues in contact with ARG 751 (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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749A GLU* 3.7 32.8 + - + +
750A LEU* 1.3 76.8 - - - +
752A GLY* 1.3 61.0 + - - +
753A ASN* 5.3 4.2 - - - +
784A TYR* 3.2 11.0 - - - -
785A GLU* 2.8 36.8 + - + +
949A ALA* 4.7 2.5 - - - -
591B PRO* 3.4 36.1 + - - +
592B GLY* 3.6 25.4 - - - +
603B THR* 3.5 34.7 + - + +
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Residues in contact with GLY 752 (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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751A ARG* 1.3 79.7 + - - +
753A ASN* 1.3 73.4 + - - +
783A THR 3.3 10.3 - - - -
784A TYR* 3.9 5.8 - - - -
949A ALA* 4.8 3.4 - - - +
950A GLN 4.7 6.2 - - - +
951A VAL* 3.6 21.1 - - - +
603B THR* 4.5 3.5 - - - +
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Residues in contact with ASN 753 (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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751A ARG* 5.3 4.8 - - - +
752A GLY* 1.3 79.6 + - - +
754A SER* 1.3 63.5 + - - +
755A PHE* 3.7 21.8 - - + -
783A THR 3.0 30.9 + - - +
951A VAL* 3.4 12.2 - - - +
603B THR* 2.7 29.6 + - - +
605B PRO* 3.5 29.1 - - - +
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Residues in contact with SER 754 (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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753A ASN* 1.3 75.7 + - - +
755A PHE* 1.3 74.8 + - - +
756A PRO 2.9 19.3 + - - +
757A ALA* 3.5 14.4 + - - +
780A VAL* 4.8 0.4 - - - -
781A GLU 3.1 9.9 - - - -
782A HIS* 3.8 2.5 - - - -
951A VAL* 3.4 9.4 - - - +
952A TRP 3.0 19.4 + - - -
953A THR* 3.0 24.7 + - - -
605B PRO* 6.0 0.5 - - - +
606B ASP* 4.5 2.4 - - - +
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Residues in contact with PHE 755 (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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753A ASN* 3.7 28.5 - - + -
754A SER* 1.3 80.5 - - - +
756A PRO* 1.3 62.5 - - - +
779A LYS* 4.9 3.4 - - - -
780A VAL* 3.7 0.7 - - - -
781A GLU* 2.7 55.4 + - + +
783A THR* 4.1 20.9 - - - -
602B PRO 3.2 27.4 - - - -
603B THR* 4.9 0.2 - - - -
604B CYS 3.2 24.7 - - - -
605B PRO* 4.8 0.7 - - + -
606B ASP* 3.7 31.0 - - + +
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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