Contacts of the strand formed by residues 81 - 91 (chain X) in PDB entry 2PKA
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 GLN 81 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66X TRP* 3.6 5.2 - - - -
67X LEU* 2.8 40.7 + - + +
79X THR 4.0 4.7 + - - +
80X ALA* 1.3 79.3 - - - +
82X PHE* 1.3 59.0 - - - +
83X PHE* 3.3 28.2 - - + -
112Y ALA* 4.0 0.2 - - - -
113Y LYS* 2.8 53.0 + - - +
115Y THR* 3.7 12.9 - - - +
118Y VAL* 3.5 21.7 - - + +
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Residues in contact with PHE 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X GLU* 3.6 36.1 - - + -
65X VAL 3.6 2.2 - - - -
66X TRP* 3.2 55.4 - + + -
81X GLN* 1.3 68.4 - - - +
83X PHE* 1.3 82.4 + - - +
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Residues in contact with PHE 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X GLU* 3.7 5.0 - - - +
65X VAL* 2.7 43.2 + - + +
67X LEU* 3.3 38.1 - - + -
81X GLN* 3.3 42.2 - - + -
82X PHE* 1.3 90.4 - - - +
84X GLY* 1.3 67.5 + - - +
108Y LEU* 4.0 19.7 - - + -
109Y GLN* 4.9 2.2 - - - -
110Y SER* 3.4 39.0 - - - -
111Y PRO 3.8 8.5 - - - -
112Y ALA* 3.7 12.6 - - + -
113Y LYS 4.6 0.2 - - - -
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Residues in contact with GLY 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X TYR 4.3 7.2 - - - -
64X GLU* 5.2 0.9 - - - -
83X PHE* 1.3 82.6 - - - +
85X VAL* 1.3 64.8 + - - +
108Y LEU* 3.8 1.6 - - - -
109Y GLN* 2.8 45.4 + - - +
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Residues in contact with VAL 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X TYR* 3.4 51.5 + - + +
65X VAL* 3.3 34.1 - - + -
84X GLY* 1.3 77.3 - - - +
86X THR* 1.3 61.7 + - - +
87X ALA 3.8 20.6 - - - +
106Y LEU* 4.3 11.4 - - + -
107Y ARG 3.5 12.1 - - - +
108Y LEU* 4.8 2.7 - - + -
109Y GLN* 4.5 1.4 - - - +
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Residues in contact with THR 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X VAL* 1.3 75.7 - - - +
87X ALA* 1.3 61.4 + - + +
107Y ARG* 2.9 40.5 + - + +
108Y LEU 3.9 9.6 - - - +
109Y GLN* 3.9 15.2 - - - +
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Residues in contact with ALA 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X VAL* 3.4 10.0 - - - +
86X THR* 1.3 84.6 - - - +
88X ASP* 1.3 60.4 + - - +
89X PHE* 3.8 26.0 - - + -
106Y LEU* 3.7 1.9 - - - -
107Y ARG* 2.8 40.7 + - + +
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Residues in contact with ASP 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X LYS* 2.8 36.9 + - - +
60X ASN 3.8 1.9 - - - +
63X TYR* 2.7 30.3 + - + +
87X ALA* 1.3 75.6 - - - +
89X PHE* 1.3 69.3 - - - +
90X PRO* 3.5 5.7 - - - +
104Y MET* 3.9 3.8 - - - -
105Y LEU 3.3 4.7 - - - -
106Y LEU* 3.4 24.7 - - + -
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Residues in contact with PHE 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X TRP* 3.5 38.1 - + - -
87X ALA* 3.8 29.2 - - + -
88X ASP* 1.3 76.9 - - - +
90X PRO* 1.3 67.0 - - - +
104Y MET* 3.3 5.0 - - - -
105Y LEU* 2.7 34.2 + - + +
107Y ARG* 4.1 3.4 - - + -
237Y TRP* 3.4 10.6 - - + -
241Y THR* 3.8 21.8 - - + -
245Y ASN* 3.7 32.8 - - + -
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Residues in contact with PRO 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ALA* 4.5 10.5 - - + -
59X LYS* 3.9 33.7 - - + +
88X ASP 3.5 9.6 - - - +
89X PHE* 1.3 91.5 - - - +
91X HIS* 1.3 68.4 + - - +
92X PRO* 3.3 8.1 - - - +
94X PHE* 5.4 2.5 - - + -
103Y LEU 3.8 1.8 - - - +
104Y MET* 3.6 18.8 - - + -
237Y TRP* 4.1 2.3 - - - -
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Residues in contact with HIS 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ALA* 4.7 0.6 - - - +
89X PHE 3.7 0.4 + - - -
90X PRO* 1.3 73.2 - - - +
92X PRO* 1.3 67.4 - - + +
93X GLY* 2.9 35.9 + - - -
94X PHE* 2.8 29.3 + - - +
101Y HIS* 3.3 43.7 + + + +
103Y LEU* 2.9 20.5 + - + +
234Y TYR* 3.9 25.7 - + - -
237Y TRP* 3.6 42.0 - + + +
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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