Contacts of the strand formed by residues 104 - 108 (chain D) in PDB entry 2CNW
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 104 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLY 5.1 0.6 - - - -
103D ARG* 1.3 77.2 - - + +
105D VAL* 1.3 63.1 + - - +
177D VAL* 4.2 23.1 - - + -
180D MET* 4.5 7.2 - - + -
188D LEU* 3.4 13.7 - - + +
190D VAL* 3.9 25.8 - - + -
213D ILE* 3.7 20.2 - - + -
220D GLU* 2.8 38.8 + - + +
221D PRO* 3.6 8.4 - - + +
222D LYS* 3.4 21.1 + - - +
223D GLU* 3.4 8.8 + - - +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PRO* 3.9 23.1 - - + -
103D ARG 4.0 0.4 + - - -
104D VAL* 1.3 74.9 - - - +
106D LEU* 1.3 60.6 + - - +
107D VAL* 3.9 8.9 + - + +
187D LEU* 4.7 5.6 - - + -
188D LEU 2.8 9.3 + - - +
189D PHE* 3.4 34.0 - - + -
190D VAL* 2.9 25.8 + - - +
223D GLU* 3.4 22.7 - - + +
225D TRP* 3.6 40.8 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL 4.0 1.0 - - - -
105D VAL* 1.3 72.0 - - - +
107D VAL* 1.3 61.3 + - - +
108D VAL* 3.9 19.3 + - + -
190D VAL* 3.6 30.3 - - + -
192D THR* 3.7 18.2 - - + -
206D LEU* 4.8 7.6 - - + +
209D VAL* 3.9 7.4 - - + -
210D LYS* 4.4 31.4 - - + +
213D ILE* 3.8 14.4 - - + -
221D PRO* 4.3 12.5 - - + +
223D GLU 2.9 12.3 + - - +
224D VAL* 3.4 16.2 - - + +
225D TRP 2.8 26.5 + - - -
247D VAL* 5.1 3.6 - - + -
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D VAL* 4.1 21.8 - - + +
106D LEU* 1.3 74.8 - - - +
108D VAL* 1.3 56.5 + - - +
115D LYS* 3.9 21.6 - - + +
118D THR* 5.5 2.9 - - + -
119D ILE* 3.8 29.2 - - + -
122D LEU* 4.9 5.4 - - + -
189D PHE* 4.7 5.2 - - + -
190D VAL 3.0 14.2 + - - +
192D THR* 2.8 36.2 + - - +
225D TRP* 3.4 9.6 - - + +
227D VAL* 3.7 28.0 - - + -
253D ILE* 6.0 0.7 - - + -
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 4.0 20.6 - - + -
107D VAL* 1.3 79.3 - - - +
109D GLY* 1.3 54.7 + - - +
115D LYS* 3.4 8.7 - - - +
192D THR* 3.8 4.7 - - - -
206D LEU* 3.7 30.5 - - + -
224D VAL* 4.3 9.2 - - + -
225D TRP 2.9 15.2 + - - +
226D LEU* 3.3 6.0 - - + -
227D VAL* 2.7 32.9 + - - +
243D PHE* 3.9 22.7 - - + -
247D VAL* 4.7 2.0 - - + -
249D LEU* 4.0 24.5 - - + -
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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