Contacts of the strand formed by residues 213 - 219 (chain A) 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 GLU 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PRO* 4.3 8.9 - - + +
94A VAL 4.7 10.8 + - - +
100A LEU 3.5 2.6 + - - -
101A TRP* 3.1 46.4 - - + +
102A PHE 3.0 21.9 + - - -
211A PRO* 3.5 5.9 - - - +
212A ASP* 1.3 84.5 - - + +
214A VAL* 1.3 63.2 + - - +
215A LEU* 4.0 11.4 - - + -
240A THR* 2.5 31.1 + - - +
268A TYR* 3.1 32.5 + - - -
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Residues in contact with VAL 214 (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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102A PHE* 3.8 11.2 - - + -
104A VAL* 3.9 32.3 - - + -
206A LYS* 4.0 15.5 - - + +
211A PRO* 3.7 24.5 - - + +
213A GLU* 1.3 78.1 - - - +
215A LEU* 1.3 61.5 + - - +
216A LEU 3.6 2.6 + - - -
237A VAL* 4.5 8.7 - - + -
238A GLY 3.5 25.6 - - - +
239A VAL* 3.7 9.0 - - + +
240A THR* 3.0 30.8 + - + +
241A GLY 3.6 3.6 + - - +
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Residues in contact with LEU 215 (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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101A TRP* 4.0 25.8 - - + -
102A PHE 2.9 18.3 + - - +
103A LEU* 3.5 11.2 - - + -
104A VAL* 2.9 28.4 + - - -
118A LEU* 4.0 16.6 - - + -
213A GLU* 4.0 19.3 - - + +
214A VAL* 1.3 75.2 - - - +
216A LEU* 1.3 62.1 + - - +
217A VAL* 3.4 2.9 + - + +
241A GLY* 3.6 9.6 - - - +
242A LEU 4.6 0.2 - - - +
243A VAL* 3.9 27.8 - - + -
268A TYR* 3.7 35.9 - - + -
269A PHE* 5.3 2.5 - - + -
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Residues in contact with LEU 216 (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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104A VAL* 3.5 6.0 - - + +
105A GLY* 3.8 25.8 - - - -
106A LEU 5.2 0.2 - - - +
214A VAL 3.6 2.0 + - - -
215A LEU* 1.3 68.5 - - - +
217A VAL* 1.3 67.0 + - - +
218A LEU* 3.5 13.7 + - + -
229A VAL* 4.9 6.3 - - + -
230A ALA* 3.9 35.0 - - + +
233A PHE* 4.3 20.4 - - + -
239A VAL* 4.0 21.1 - - + -
241A GLY 3.0 14.5 + - - +
242A LEU* 3.5 24.9 - - + +
243A VAL 3.0 23.1 + - - +
263A THR* 5.8 0.9 - - + -
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Residues in contact with VAL 217 (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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103A LEU* 4.1 21.3 - - + -
104A VAL 2.9 11.6 + - - +
105A GLY* 4.3 3.1 - - - -
106A LEU* 4.6 1.4 + - - +
109A SER* 3.0 34.0 + - - +
110A GLY 3.9 12.3 - - - +
111A LYS* 3.6 24.0 - - + -
114A THR* 4.2 3.4 - - + +
215A LEU 3.9 12.1 - - - +
216A LEU* 1.3 78.7 - - - +
218A LEU* 1.3 59.4 + - - +
243A VAL* 3.5 17.5 - - + +
245A THR* 3.5 31.0 - - + -
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Residues in contact with LEU 218 (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 LEU* 5.8 3.6 - - + -
109A SER* 4.7 0.4 - - - -
216A LEU* 3.5 16.6 + - + +
217A VAL* 1.3 76.6 - - - +
219A ASP* 1.3 64.3 + - - +
222A THR* 4.1 24.0 - - + +
226A ALA* 4.7 9.9 - - + +
229A VAL* 5.0 14.4 - - + -
230A ALA* 6.1 0.4 - - + +
242A LEU* 4.1 12.1 - - + -
243A VAL 2.8 12.4 + - - +
244A LEU* 3.3 16.8 - - + +
245A THR* 2.8 32.3 + - - -
255A ALA* 3.6 34.8 - - + +
256A ALA* 4.3 1.1 - - - +
259A ALA* 4.0 16.4 - - + -
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Residues in contact with ASP 219 (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 GLY 4.7 0.7 - - - +
109A SER* 4.2 16.6 - - - -
218A LEU* 1.3 77.8 - - - +
220A ALA* 1.3 73.0 + - - +
221A MET* 3.2 40.4 + - - +
222A THR* 2.8 36.2 + - - +
244A LEU* 4.3 0.6 - - - +
245A THR* 3.3 10.7 + - - +
246A LYS* 2.8 39.0 + - - +
255A ALA* 4.7 1.2 - - - +
111D ASN 4.5 0.7 - - - +
229D ASP* 5.5 2.4 - - - +
231D VAL* 6.2 2.2 - - + -
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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