Contacts of the strand formed by residues 163 - 168 (chain D) in PDB entry 3CJC
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 163 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA* 3.4 29.4 - - + +
131D VAL* 3.8 26.2 - - + -
151D TYR* 3.4 32.1 - - + -
154D VAL* 3.9 9.2 - - + -
160D LEU 3.4 18.2 - - - +
161D ASN 3.4 1.6 + - - -
162D ASP* 1.3 80.2 - - - +
164D MET* 1.3 63.5 + - - +
165D LEU* 3.7 9.2 - - + +
216D VAL* 3.6 1.0 - - - -
217D ALA 2.9 29.1 + - - -
221D LEU* 3.2 10.1 - - - +
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Residues in contact with MET 164 (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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3D ILE* 4.0 27.4 - - + -
128D PHE* 5.2 2.7 - - + -
129D ALA 2.8 15.4 + - - +
130D ILE* 3.1 11.0 - - + +
131D VAL 2.7 31.3 + - - +
163D VAL* 1.3 72.0 - - - +
165D LEU* 1.3 56.4 + - - +
166D MET* 3.7 37.8 + - + +
214D ILE* 4.0 7.6 - - + -
215D VAL 3.5 10.5 - - - +
216D VAL* 3.8 22.0 - - + -
221D LEU* 3.7 8.7 - - + +
225D VAL* 5.7 0.4 - - + -
257D VAL* 3.9 24.9 - - + -
259D LEU* 4.5 11.4 - - + -
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Residues in contact with LEU 165 (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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131D VAL* 3.4 27.4 - - + +
147D LEU* 4.1 35.9 - - + +
151D TYR* 4.4 12.8 - - + +
163D VAL* 3.7 25.1 - - + +
164D MET* 1.3 72.1 - - - +
166D MET* 1.3 59.7 + - - +
169D PHE* 3.7 18.4 - - + -
186D LEU* 4.3 10.8 - - + -
192D PHE* 4.2 11.7 - - + -
214D ILE* 3.8 0.2 - - - -
215D VAL* 2.8 59.1 + - + +
216D VAL 4.7 0.2 - - - +
217D ALA* 4.8 2.0 - - + +
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Residues in contact with MET 166 (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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3D ILE* 3.5 27.1 - - + -
4D ALA* 4.2 3.6 - - - +
5D ALA* 3.8 20.0 - - + -
34D ILE* 5.0 4.0 - - + -
36D LEU* 4.1 24.3 - - + +
82D PHE* 4.9 1.6 - - + -
130D ILE* 3.4 31.0 - - + -
131D VAL 3.1 8.0 + - - +
132D ALA* 3.5 5.1 - - - +
133D LEU 3.3 20.1 + - - -
164D MET* 3.7 20.2 - - + +
165D LEU* 1.3 74.4 - - - +
167D GLY* 1.3 58.0 + - - +
169D PHE* 3.6 7.6 - - - -
213D ARG 3.4 12.3 - - - +
214D ILE* 4.0 20.0 - - + -
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Residues in contact with GLY 167 (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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5D ALA* 3.9 7.2 - - - +
36D LEU* 4.8 0.7 - - - -
38D GLN* 3.5 17.0 - - - -
133D LEU 3.4 9.0 - - - -
166D MET* 1.3 75.3 - - - +
168D ASP* 1.3 61.8 + - - -
169D PHE* 3.0 11.7 + - - -
212D ASP* 4.2 4.5 - - - -
213D ARG 2.9 31.3 + - - -
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Residues in contact with ASP 168 (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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7D ASN* 3.0 27.4 + - + +
38D GLN* 2.9 24.5 + - - +
133D LEU 3.4 1.2 + - - -
134D HIS* 3.3 12.7 + - + -
135D SER* 3.1 22.2 + - - -
167D GLY* 1.3 66.5 - - - -
169D PHE* 1.3 59.9 + - - +
170D ASN* 3.0 26.3 + - - +
211D TYR* 3.3 12.6 - - - +
212D ASP* 3.3 13.5 + - - +
252D HIS* 3.2 26.9 + - - -
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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