Contacts of the strand formed by residues 189 - 196 (chain A) in PDB entry 2PJ7
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 ILE 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ALA* 3.4 5.6 - - + +
63A PHE* 4.1 14.4 - - + +
106A TYR* 3.8 30.5 - - + -
182A PHE* 4.6 1.1 - - + -
183A ILE* 4.0 38.4 - - + +
186A ASN* 3.3 23.9 + - + +
187A LEU 3.3 12.7 + - - +
188A SER* 1.3 76.5 - - - +
190A LYS* 1.3 63.2 + - - +
191A ALA 3.4 23.8 - - - +
192A TYR* 5.2 0.4 - - + -
263A ILE* 3.7 33.1 - - + +
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Residues in contact with LYS 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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60A PRO* 4.0 24.0 - - + -
61A ALA 2.8 11.1 + - - +
62A ILE* 5.4 0.9 - - + -
187A SER 3.1 25.7 + - - -
188A SER* 3.6 13.2 - - - +
189A ILE* 1.3 77.8 + - - +
191A ALA* 1.3 61.4 + - - +
263A ILE* 3.8 9.9 - - - +
264A LYS 4.3 3.2 + - - -
265A TYR* 3.6 21.6 + - + +
304A VAL* 3.9 19.3 - - + -
308A LEU* 4.0 20.4 - - + +
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Residues in contact with ALA 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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61A ALA 3.9 2.2 + - - -
62A ILE* 3.7 21.5 - - + -
63A PHE 3.0 24.7 + - - -
189A ILE* 3.4 7.5 - - - +
190A LYS* 1.3 82.7 - - - +
192A TYR* 1.3 62.2 + - - +
193A LEU* 5.1 6.5 - - + -
263A ILE* 3.6 5.1 - - - +
265A TYR* 3.1 22.2 - - + +
300A VAL* 5.3 1.8 - - + -
304A VAL* 4.1 15.9 - - + -
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Residues in contact with TYR 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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63A PHE* 3.4 27.4 - + + -
65A ASP* 2.6 30.2 + - - -
68A PHE* 3.9 2.1 - - - -
179A LEU* 4.5 3.0 - - + +
183A ILE* 3.8 22.2 - - + -
191A ALA* 1.3 74.1 - - - +
193A LEU* 1.3 67.4 + - - +
194A THR* 3.5 20.0 - - + -
254A SER* 2.8 38.6 + - - -
255A ASP* 3.8 12.8 - - + -
257A TRP* 6.5 0.2 - + - -
258A ALA* 3.7 20.9 - - + -
263A ILE* 3.7 12.1 - - + +
265A TYR 2.8 6.9 + - - -
266A SER* 3.3 19.5 - - - +
267A PHE 3.0 25.5 + - - -
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Residues in contact with LEU 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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62A ILE* 3.9 24.7 - - + -
63A PHE 2.9 10.9 + - - +
64A MET* 3.1 20.3 - - + +
65A ASP* 3.0 25.6 + - - +
105A PHE* 6.2 0.4 - - + -
191A ALA* 5.1 2.7 - - + -
192A TYR* 1.3 89.2 - - - +
194A THR* 1.3 61.0 + - - +
195A ILE* 5.0 2.7 - - + -
267A PHE* 3.4 31.9 - - + +
269A PHE* 4.2 13.7 - - + -
297A ILE* 4.0 33.0 - - + +
300A VAL* 4.4 18.2 - - + -
301A THR* 5.6 0.2 - - - +
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Residues in contact with THR 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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65A ASP* 2.7 23.4 + - - -
68A PHE* 3.9 4.7 - - - -
144A ASN* 5.8 0.9 - - - +
192A TYR* 3.5 24.2 + - + -
193A LEU* 1.3 74.7 - - - +
195A ILE* 1.3 63.7 + - - +
196A HIS* 3.4 18.0 + - + +
254A SER* 3.9 7.9 + - - +
255A ASP* 4.4 1.8 - - + -
267A PHE 3.0 9.7 + - - +
268A THR* 3.2 30.8 - - + +
269A PHE* 2.9 24.8 + - - +
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Residues in contact with ILE 195 (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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64A MET* 4.1 22.4 - - + -
65A ASP* 3.0 18.5 + - - +
66A CYS* 3.8 13.1 - - - -
67A GLY 4.2 6.2 + - - -
68A PHE 4.9 2.6 + - - -
72A GLU* 4.6 0.3 - - - +
75A SER* 2.9 36.8 + - - +
78A PHE* 4.2 15.3 - - + -
193A LEU* 4.9 0.9 - - + -
194A THR* 1.3 79.2 + - - +
196A HIS* 1.3 71.6 + - - +
269A PHE* 3.8 27.6 - - + +
271A LEU* 3.6 33.7 - - + -
293A THR* 5.3 1.3 - - + -
297A ILE* 4.5 5.2 - - + -
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Residues in contact with HIS 196 (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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68A PHE* 3.7 21.1 - - + +
69A HIS* 3.4 17.3 - + - -
72A GLU* 3.1 8.8 + - - +
75A SER* 4.4 6.7 - - - -
144A ASN* 3.8 20.7 + - - -
194A THR* 3.4 23.7 + - - +
195A ILE* 1.3 83.2 - - - +
197A SER* 1.3 63.1 + - - +
268A THR* 3.9 16.1 - - + +
269A PHE 2.7 11.6 + - - +
270A GLU* 3.4 21.8 - - - +
271A LEU* 2.9 28.4 + - - +
400A ZN 2.1 31.6 - - - -
401A 235 3.3 4.0 + - + +
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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