Contacts of the strand formed by residues 655 - 662 (chain A) in PDB entry 2DFS
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 THR 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLN* 5.0 9.8 - - + +
153A ASP* 5.9 1.0 - - - -
155A ARG* 3.0 25.2 + - - +
156A ASN 3.3 0.2 + - - -
157A GLN* 2.8 30.4 + - - +
158A SER 3.1 19.3 + - - -
468A HIS* 3.3 27.8 - - + +
654A THR* 1.3 73.8 - - - +
656A PRO* 1.3 62.4 - - + +
657A HIS* 3.6 9.1 + - + -
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Residues in contact with PRO 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 5.6 0.2 - - - +
158A SER* 3.2 13.2 - - - +
160A ILE* 4.0 13.9 - - + -
464A GLN* 4.1 15.0 - - + +
468A HIS* 3.3 41.4 - - + +
651A LEU 5.0 4.3 - - - +
654A THR 3.8 7.6 - - - +
655A THR* 1.3 86.6 - - + +
657A HIS* 1.3 64.2 + - - +
658A TYR* 3.4 38.0 - - + +
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Residues in contact with HIS 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE 5.7 0.2 - - - -
142A VAL* 3.9 23.5 + - + +
145A GLU* 4.5 5.4 - - - +
146A ALA* 3.6 33.8 + - + +
149A GLN* 3.5 25.1 + - - -
157A GLN* 3.4 27.1 - - + +
158A SER 2.8 24.7 + - - +
159A ILE* 3.6 10.3 - - + +
160A ILE* 2.7 34.1 + - - +
655A THR* 3.6 12.8 + - + -
656A PRO* 1.3 75.3 + - - +
658A TYR* 1.4 60.1 + - - +
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Residues in contact with TYR 658 (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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105A ILE* 4.0 22.8 + - + +
106A VAL* 3.7 14.8 - - + -
107A LEU* 3.0 24.4 + - - +
142A VAL* 5.0 3.5 - - - +
160A ILE* 3.6 31.2 - - + -
461A LEU* 4.7 4.6 + - + -
464A GLN* 3.5 13.7 + - - +
465A PHE* 3.6 54.1 + + + -
468A HIS* 4.1 9.1 - - - +
656A PRO* 3.4 44.9 - - + +
657A HIS* 1.4 74.4 - - - +
659A VAL* 1.3 63.9 + - - +
660A ARG* 3.9 17.5 - - - +
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Residues in contact with VAL 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 5.8 0.2 - - + -
107A LEU* 3.4 24.5 - - + +
109A ALA* 4.3 13.7 - - + -
139A ILE* 3.8 26.0 - - + -
142A VAL* 4.4 7.6 - - + -
159A ILE* 4.4 16.4 - - + -
160A ILE 3.0 11.2 + - - +
161A VAL* 3.5 11.1 - - + +
162A SER* 3.0 25.8 + - - +
172A SER* 4.5 5.6 - - - +
658A TYR* 1.3 77.0 - - - +
660A ARG* 1.3 67.1 + - - +
661A CYS* 4.1 21.3 - - - -
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Residues in contact with ARG 660 (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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106A VAL* 3.6 24.3 - - + +
107A LEU 2.8 12.5 + - - +
108A VAL* 3.5 8.8 - - + +
109A ALA 2.9 26.1 + - - +
160A ILE* 6.1 0.4 - - - +
162A SER* 3.1 28.8 + - - -
441A PHE* 6.3 0.2 - - - -
462A GLN* 2.9 29.1 + - - +
465A PHE* 4.4 14.6 - - - +
658A TYR* 3.9 29.1 - - - +
659A VAL* 1.3 73.3 - - - +
661A CYS* 1.3 62.2 + - - +
662A ILE* 4.2 2.2 - - + +
685A CYS* 2.8 48.9 + - - -
686A GLY* 4.3 3.8 - - - -
687A VAL* 4.3 10.7 - - + +
690A THR* 5.2 1.8 + - - -
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Residues in contact with CYS 661 (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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109A ALA* 3.4 9.6 - - - +
161A VAL* 3.8 14.1 - - - -
162A SER 2.8 14.2 + - - +
163A GLY* 3.5 14.4 - - - -
164A GLU 4.3 1.0 + - - -
167A ALA* 3.4 33.0 - - + +
168A GLY 4.0 1.8 - - - -
169A LYS* 3.8 26.0 - - + -
172A SER* 3.5 24.9 - - - -
659A VAL* 4.1 6.5 - - - -
660A ARG* 1.3 74.9 - - - +
662A ILE* 1.3 65.3 + - - +
681A GLN* 4.6 1.0 - - - +
685A CYS* 4.8 0.3 - - - -
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Residues in contact with ILE 662 (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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108A VAL* 3.9 26.9 - - + -
109A ALA 2.8 12.0 + - - +
110A ILE* 3.6 15.3 - - + -
111A ASN* 3.0 28.9 + - - +
167A ALA* 3.9 5.0 + - - +
660A ARG* 4.2 2.5 - - + +
661A CYS* 1.3 82.2 - - - +
663A LYS* 1.4 72.5 + - - +
664A PRO* 3.6 2.6 - - + +
673A PHE* 6.4 1.3 - - + -
678A ALA* 5.0 9.2 - - + +
681A GLN* 3.8 30.3 - - + +
682A LEU* 4.1 20.4 - - + -
685A CYS* 4.0 22.2 - - - -
687A VAL* 5.2 0.2 - - + -
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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