Contacts of the strand formed by residues 196 - 199 (chain A) in PDB entry 3DAG
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 ASN 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLY* 2.8 30.3 + - - -
170A ALA 2.9 14.2 + - - +
171A ILE* 3.3 10.4 - - + +
172A VAL 2.9 24.1 + - - +
194A ASP 4.1 3.9 + - - +
195A LEU* 1.3 70.2 - - - +
197A ILE* 1.3 63.6 - - - +
198A THR 3.8 0.3 + - - -
219A ALA* 3.7 8.1 - - + +
220A SER* 3.0 33.4 + - - -
223A ALA* 3.6 27.4 - - + +
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Residues in contact with ILE 197 (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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172A VAL* 3.4 17.0 - - + -
180A THR* 4.4 7.6 - - + -
183A PHE* 3.5 27.1 - - + -
184A ALA* 3.8 29.8 - - + +
187A PHE* 3.8 27.1 - - + -
192A ARG 5.6 0.7 - - - +
195A LEU* 3.8 31.9 - - + +
196A ASN* 1.3 70.3 - - - +
198A THR* 1.3 68.1 + - - +
215A ALA 4.6 0.9 - - - +
218A TYR* 3.1 43.0 + - + +
219A ALA* 3.4 1.6 - - - +
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Residues in contact with THR 198 (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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171A ILE* 3.8 12.6 - - + -
172A VAL 3.1 4.3 + - - +
173A THR* 3.2 22.5 - - + -
174A HIS* 3.2 20.3 - - - -
180A THR* 4.5 5.6 - - - -
196A ASN 4.5 0.9 - - - +
197A ILE* 1.3 78.6 - - - +
199A SER* 1.3 64.4 + - - +
214A ILE* 3.3 10.5 - - + +
215A ALA* 2.6 34.7 + - - -
219A ALA* 4.4 9.4 - - + -
223A ALA 5.8 0.7 - - - +
224A VAL* 4.9 4.5 - - + -
227A LEU* 3.4 30.5 - - + -
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Residues in contact with SER 199 (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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173A THR* 3.9 2.5 - - - -
174A HIS* 3.4 34.8 - - - +
198A THR* 1.3 82.4 + - - +
200A TYR* 1.3 61.8 + - - +
201A HIS* 4.2 7.0 - - - -
213A TYR 2.7 27.2 + - - +
214A ILE* 3.5 10.0 - - - +
215A ALA* 2.8 26.1 + - - +
227A LEU* 3.5 15.1 - - - +
246A ILE* 3.8 6.6 - - - +
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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