Contacts of the strand formed by residues 655 - 662 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149M GLN* 4.9 9.0 - - + +
153M ASP* 5.9 0.9 - - - -
155M ARG* 3.0 24.4 + - - +
156M ASN 3.3 0.2 + - - -
157M GLN* 2.8 30.1 + - - +
158M SER 3.1 19.2 + - - -
468M HIS* 3.3 28.3 - - + +
654M THR* 1.3 72.8 - - - +
656M PRO* 1.3 63.1 - - - +
657M HIS* 3.6 8.9 + - + -
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Residues in contact with PRO 656 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M ILE* 5.6 0.2 - - - +
158M SER* 3.2 13.5 - - - +
160M ILE* 4.0 13.2 - - + -
464M GLN* 4.2 16.2 - - + +
468M HIS* 3.2 48.0 - - + +
651M LEU 5.0 4.7 - - - +
654M THR 3.8 7.2 - - - +
655M THR* 1.3 86.9 - - - +
657M HIS* 1.3 63.4 + - - +
658M TYR* 3.4 35.8 - - + +
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Residues in contact with HIS 657 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M ILE 5.6 0.2 - - - -
142M VAL* 3.9 24.2 + - + +
145M GLU* 4.5 5.4 - - - +
146M ALA* 3.6 32.5 + - + +
149M GLN* 3.5 25.6 + - - -
157M GLN* 3.4 28.3 - - + +
158M SER 2.8 23.7 + - - +
159M ILE* 3.6 10.3 - - + +
160M ILE* 2.7 35.3 + - - +
655M THR* 3.6 13.0 + - + -
656M PRO* 1.3 76.1 + - - +
658M TYR* 1.4 59.6 + - - +
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Residues in contact with TYR 658 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M ILE* 4.0 17.7 + - + +
106M VAL* 3.6 20.2 - - + -
107M LEU* 3.0 25.6 + - - +
142M VAL* 5.0 3.9 - - - +
160M ILE* 3.6 31.6 - - + -
461M LEU* 4.7 4.8 + - + -
464M GLN* 3.5 12.3 + - - +
465M PHE* 3.6 54.6 + + + -
468M HIS* 4.1 8.7 - - - -
656M PRO* 3.4 46.9 - - + +
657M HIS* 1.4 73.7 - - - +
659M VAL* 1.3 64.2 + - - +
660M ARG* 3.9 16.6 - - - +
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Residues in contact with VAL 659 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M TYR* 5.7 0.4 - - + -
107M LEU* 3.4 25.1 - - + +
109M ALA* 4.3 13.7 - - + -
139M ILE* 3.8 25.8 - - + -
142M VAL* 4.4 7.4 - - + -
159M ILE* 4.3 16.6 - - + -
160M ILE 3.0 11.1 + - - +
161M VAL* 4.3 11.9 - - + -
162M SER* 3.0 26.3 + - - +
172M SER* 4.5 5.2 - - - +
658M TYR* 1.3 77.1 - - - +
660M ARG* 1.3 66.5 + - - +
661M CYS* 4.1 21.3 - - - -
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Residues in contact with ARG 660 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M VAL* 3.6 24.1 - - + +
107M LEU 2.8 13.1 + - - +
108M VAL* 3.4 8.9 - - + +
109M ALA 2.9 26.2 + - - +
160M ILE* 6.1 0.6 - - - +
162M SER* 3.1 29.4 + - - -
462M GLN* 2.9 30.3 + - - +
465M PHE* 4.4 13.3 - - - +
658M TYR* 3.9 29.9 - - - +
659M VAL* 1.3 71.7 - - - +
661M CYS* 1.3 61.4 - - - +
662M ILE* 4.0 3.0 + - + +
685M CYS* 2.8 46.9 + - - -
686M GLY* 4.3 4.2 - - - -
687M VAL* 4.3 12.3 - - + +
690M THR* 5.2 1.6 + - - -
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Residues in contact with CYS 661 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M ALA* 3.4 9.4 - - - -
161M VAL* 3.8 14.6 - - - -
162M SER 2.8 14.0 + - - +
163M GLY* 3.5 14.7 - - - -
164M GLU 4.3 1.0 + - - -
167M ALA* 3.5 33.3 - - + +
168M GLY 4.0 1.8 - - - -
169M LYS* 3.8 24.9 - - + -
172M SER* 3.5 24.2 - - - -
659M VAL* 4.1 6.7 - - - -
660M ARG* 1.3 74.0 - - - +
662M ILE* 1.3 66.3 + - - +
681M GLN* 4.6 1.2 - - - +
685M CYS* 4.7 0.5 - - - -
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Residues in contact with ILE 662 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M LEU* 6.3 0.2 - - + -
108M VAL* 3.9 25.6 - - + -
109M ALA 2.8 11.6 + - - +
110M ILE* 3.6 15.1 - - + -
111M ASN* 3.0 28.6 + - - +
167M ALA* 3.8 5.0 + - - +
660M ARG* 4.2 2.5 - - + +
661M CYS* 1.3 82.8 - - - +
663M LYS* 1.4 74.1 + - - +
664M PRO* 3.6 2.4 - - + +
673M PHE* 6.4 1.3 - - + -
678M ALA* 5.0 10.1 - - + +
681M GLN* 3.8 28.9 - - + +
682M LEU* 4.1 20.6 - - + -
685M CYS* 4.0 22.2 - - - -
687M VAL* 5.2 0.4 - - + -
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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