Contacts of the strand formed by residues 189 - 193 (chain A) in PDB entry 4WPN
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 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 2.9 35.6 + - - +
70A ALA* 4.0 10.3 - - + -
71A PHE* 4.0 14.0 - - + +
77A TRP* 3.9 18.6 - - + -
161A GLY 3.2 5.4 + - - +
162A VAL* 3.4 11.2 - - - +
163A CYS* 2.9 24.9 + - - +
188A ASN* 1.3 76.9 - - - +
190A VAL* 1.3 68.8 + - - +
217A GLY 3.9 5.6 - - - -
218A VAL* 3.4 21.8 - - - -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS* 3.3 9.6 - - + +
165A GLN* 3.5 25.8 - - - +
180A ILE* 4.3 6.3 - - + -
183A ALA* 3.8 24.7 - - + -
184A LEU* 4.7 9.0 - - + -
189A THR* 1.3 83.6 - - - +
191A VAL* 1.3 63.3 + - - +
192A VAL* 3.9 12.1 - - + -
218A VAL 2.9 17.5 + - - +
219A VAL* 3.8 26.7 - - + -
220A ASN* 3.0 33.8 + - - -
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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
----------------------------------------------------------
60A VAL* 4.9 4.3 - - + -
63A ALA* 3.7 47.6 - - + +
64A VAL* 4.0 12.1 - - + +
67A ALA* 3.9 11.4 - - + -
162A VAL* 4.1 10.5 - - + -
163A CYS 3.0 6.8 + - - +
164A GLY* 3.3 7.3 - - - -
165A GLN 2.9 25.6 + - - +
190A VAL* 1.3 76.9 - - - +
192A VAL* 1.3 62.0 + - - +
193A LYS 4.1 0.2 + - - -
220A ASN* 3.5 4.7 - - - +
222A VAL* 4.5 11.2 - - + -
233A ILE* 4.4 21.6 - - + +
239A ILE* 5.2 1.1 - - + -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLN* 3.3 13.0 - - + +
167A ILE* 3.6 28.5 - - + -
176A LEU* 3.7 15.7 - - + -
180A ILE* 3.9 26.7 - - + -
190A VAL* 3.9 12.6 - - + -
191A VAL* 1.3 77.7 - - - +
193A LYS* 1.3 62.3 + - - +
194A PRO* 3.6 10.7 - - + +
219A VAL* 4.6 1.3 - - + -
220A ASN 2.9 15.8 + - - +
221A ILE* 3.5 14.2 - - + -
222A VAL* 2.8 31.0 + - - +
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Residues in contact with LYS 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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165A GLN 2.9 11.1 + - - +
166A ILE* 3.6 15.9 - - + +
167A ILE 3.1 20.9 + - - +
191A VAL 4.1 0.6 + - - -
192A VAL* 1.3 73.9 - - - +
194A PRO* 1.3 98.9 + - - +
195A ALA* 3.7 2.8 - - - +
196A GLU* 3.3 14.6 + - - +
222A VAL* 3.5 17.7 - - + +
224A GLY 2.9 24.9 + - - +
225A TYR 3.5 22.0 - - - -
226A GLY* 3.6 7.6 - - - +
229A ALA* 4.0 13.7 - - + -
230A GLY* 4.0 16.2 - - - +
233A ILE* 3.7 20.2 - - + -
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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