Contacts of the strand formed by residues 190 - 194 (chain A) in PDB entry 4N9W
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A TYR* 3.8 10.5 - - + -
186A ARG* 3.3 27.0 + - - +
189A ARG* 1.3 80.8 + - - +
191A VAL* 1.3 65.7 + - - +
192A LEU 4.1 0.2 - - - -
221A VAL* 4.8 0.2 - - - -
222A GLU* 3.3 17.7 - - + +
224A LEU* 3.7 30.3 - - + -
262A SER 4.7 1.1 - - - -
263A ALA* 3.9 17.2 - - + -
264A ASP* 2.9 35.9 + - - +
265A VAL* 3.3 8.7 + - - +
327A LEU* 5.7 0.2 - - - -
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Residues in contact with VAL 191 (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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190A THR* 1.3 73.7 - - - +
192A LEU* 1.3 58.0 + - - +
207A LEU* 4.5 14.8 - - + -
214A LEU* 4.0 24.9 - - + -
221A VAL* 4.4 7.4 - - + -
222A GLU 2.9 4.2 + - - -
223A ILE* 3.3 17.3 - - + +
224A LEU 2.8 31.2 + - - +
265A VAL* 3.4 27.1 - - + +
267A CYS* 3.6 30.1 - - + -
323A LEU* 4.1 9.0 - - + -
327A LEU* 4.5 7.2 - - + -
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Residues in contact with LEU 192 (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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190A THR 4.1 0.8 - - - -
191A VAL* 1.3 74.7 - - - +
193A PHE* 1.3 72.9 + - - +
194A LEU* 5.0 7.2 - - + -
224A LEU* 3.2 33.2 - - + +
226A VAL* 3.9 20.9 - - + -
256A LYS 5.4 0.4 - - - +
259A ALA* 4.2 3.1 - - + +
260A MET* 3.5 55.0 - - + +
263A ALA* 3.6 17.0 - - + +
265A VAL 2.8 12.0 + - - +
266A TYR* 3.4 10.6 - - + -
267A CYS* 2.9 29.3 + - - +
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Residues in contact with PHE 193 (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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191A VAL 4.0 0.6 + - - -
192A LEU* 1.3 77.6 - - - +
194A LEU* 1.3 69.9 + - - +
195A GLY* 3.8 19.7 - - - -
197A TYR* 3.7 20.0 - - + -
202A LYS* 3.4 39.9 - - + -
204A MET* 3.5 42.2 - - + -
207A LEU* 4.0 19.5 - - + -
223A ILE* 4.8 0.7 - - + -
224A LEU 2.9 10.3 + - - +
225A ILE* 3.5 11.8 - - + -
226A VAL 2.8 25.8 + - - -
267A CYS 4.2 4.9 - - - +
269A PRO* 3.8 24.2 - - + -
270A HIS* 6.2 1.1 - + - -
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Residues in contact with LEU 194 (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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192A LEU* 4.9 6.7 - - + -
193A PHE* 1.3 85.6 - - - +
195A GLY* 1.3 58.7 + - - +
202A LYS* 4.9 6.1 + - - +
226A VAL* 3.2 24.5 - - + -
256A LYS* 3.6 33.7 - - + +
260A MET* 4.7 9.0 - - + -
266A TYR* 4.0 26.7 + - + -
270A HIS* 5.3 4.9 + - - -
279A VAL* 4.0 20.8 - - + +
282A GLU* 5.0 0.2 - - - +
401A GDP 3.3 45.8 - - + +
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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