Contacts of the strand formed by residues 185 - 192 (chain A) in PDB entry 4P22
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 LYS 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLN 3.2 16.9 + - - +
161A VAL* 3.3 5.7 - - - +
162A VAL* 2.8 31.5 + - - +
183A GLY 4.5 6.3 - - - +
184A ILE* 1.3 73.6 - - - +
186A LEU* 1.3 55.9 + - - +
201A ASP 3.7 4.0 - - - -
202A PHE* 3.8 29.6 - - + +
205A GLU 5.3 0.4 - - - -
206A MET* 3.1 44.6 - - - +
411A LYS 4.5 1.2 + - - -
412A ALA* 3.1 52.0 + - + +
414A SER* 5.7 1.0 - - - +
416A LYS* 5.2 1.4 - - - +
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Residues in contact with LEU 186 (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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162A VAL* 3.2 35.0 - - + +
164A LEU* 4.2 16.8 - - + -
175A VAL* 4.7 0.4 - - + -
176A GLY* 3.7 26.7 - - - +
179A CYS* 4.2 16.4 - - + -
184A ILE 3.6 2.9 + - - +
185A LYS* 1.3 71.5 - - - +
187A VAL* 1.3 69.5 + - - +
188A VAL* 4.0 19.5 - - + -
199A PHE* 4.6 5.7 - - + -
200A CYS* 3.4 6.4 - - - +
201A ASP* 3.0 45.7 + - + +
202A PHE* 4.2 1.1 - - - -
306A LEU* 4.5 15.0 - - + -
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Residues in contact with VAL 187 (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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161A VAL* 4.9 5.8 - - + -
162A VAL 2.9 12.9 + - - +
163A VAL* 3.1 21.3 - - + +
164A LEU 2.8 31.5 + - - -
185A LYS 4.1 0.2 + - - -
186A LEU* 1.3 79.2 - - - +
188A VAL* 1.3 60.2 + - - +
189A ALA* 5.0 0.2 - - + -
198A LEU* 4.0 20.0 - - + -
199A PHE 3.4 8.3 - - - +
200A CYS* 4.1 2.2 - - - -
202A PHE* 3.9 20.2 - - + -
405A ALA* 4.3 11.4 - - + +
408A GLU* 4.0 21.5 - - + -
409A VAL* 4.3 14.1 - - + +
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Residues in contact with VAL 188 (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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164A LEU* 3.6 30.3 - - + +
172A GLN* 3.3 33.2 - - - +
186A LEU* 4.0 22.8 - - + -
187A VAL* 1.3 76.1 - - - +
189A ALA* 1.3 65.7 + - - +
190A ASP* 5.6 0.4 - - + -
197A GLN* 4.0 13.4 - - - +
198A LEU* 3.4 4.5 - - - +
199A PHE* 2.7 55.0 + - + +
306A LEU* 4.4 8.7 - - + -
423A TRP* 6.1 1.1 - - + -
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Residues in contact with ALA 189 (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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83A LEU* 3.6 19.6 - - + +
87A ILE* 4.1 22.0 - - + -
163A VAL* 5.2 0.9 - - + -
164A LEU 3.0 17.1 + - - +
165A THR* 3.8 10.3 - - - +
166A ASN 4.5 1.2 + - - -
187A VAL* 4.2 2.7 - - + -
188A VAL* 1.3 78.6 - - - +
190A ASP* 1.3 65.0 + - - +
197A GLN 3.5 6.7 - - - +
198A LEU* 4.3 4.5 - - + -
401A ILE* 4.6 4.5 - - + -
405A ALA* 4.1 15.3 - - + -
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Residues in contact with ASP 190 (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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83A LEU* 3.4 8.1 - - - +
166A ASN* 5.2 7.9 + - - -
172A GLN* 5.5 3.7 + - - +
188A VAL* 5.6 1.3 - - + -
189A ALA* 1.3 77.6 - - - +
191A THR* 1.3 83.3 + - - +
192A ARG* 2.8 31.8 + - - -
196A GLY* 3.2 3.8 - - - -
197A GLN* 2.8 56.5 + - - +
333A PHE* 3.4 19.6 - - + -
337A HIS* 4.3 6.6 + - - -
401A ILE* 4.5 2.6 - - - +
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Residues in contact with THR 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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81A ARG* 5.6 4.3 + - - -
83A LEU* 3.8 10.3 - - - +
190A ASP* 1.3 83.8 + - - +
192A ARG* 1.3 68.7 + - - +
193A GLY 3.9 20.9 + - - +
195A PHE 3.3 3.1 - - - -
392A GLY 4.6 7.6 - - - +
393A ASP* 4.9 5.4 - - - +
394A LEU 5.0 3.1 - - - +
397A ILE* 3.8 20.8 - - + +
398A ASN* 3.1 29.9 + - - +
401A ILE* 4.0 14.9 - - - +
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Residues in contact with ARG 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 ASP* 2.8 25.6 + - - +
191A THR* 1.3 79.1 + - - +
193A GLY* 1.3 59.0 + - - +
194A LEU 3.2 0.7 + - - -
195A PHE* 2.7 36.3 + - - +
333A PHE* 3.5 30.3 - - + -
336A LEU* 3.4 42.1 - - + +
337A HIS* 4.0 21.2 + - - -
340A CYS* 3.8 22.9 - - - +
346A PRO* 4.7 10.1 - - - +
386A LEU* 4.3 5.0 - - + +
389A VAL 3.5 9.5 - - - +
390A ALA* 4.4 14.5 + - - +
392A GLY 4.6 0.2 - - - -
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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