Contacts of the strand formed by residues 65 - 69 (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 VAL 65 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X VAL* 3.5 15.3 - - + -
32X ALA 3.6 2.9 - - - -
33X ILE* 4.6 5.8 - - + -
52X VAL* 4.4 2.9 - - + -
63X TYR* 4.8 1.1 - - + -
64X GLU* 1.3 79.5 - - - +
66X TRP* 1.3 63.1 + - - +
67X LEU* 3.4 27.4 - - + -
81X GLN 3.9 0.7 - - - +
82X PHE* 3.6 2.5 - - - -
83X PHE* 2.7 48.4 + - + +
85X VAL* 3.3 30.5 - - + -
106Y LEU* 4.4 15.3 - - + -
108Y LEU* 3.9 18.2 - - + -
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Residues in contact with TRP 66 (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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30X GLN 4.5 0.5 - - - +
31X VAL* 3.7 5.4 - - - +
32X ALA* 2.8 43.4 + - + +
34X TYR* 3.4 34.0 - + - -
65X VAL* 1.3 75.3 - - - +
67X LEU* 1.3 61.8 + - - +
70X ARG* 3.4 45.8 - - + +
80X ALA* 3.8 22.2 - - + -
81X GLN 3.6 17.9 - - - -
82X PHE* 3.2 53.5 - + + -
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Residues in contact with LEU 67 (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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28X PRO 6.0 0.7 - - - +
30X GLN 4.7 5.4 - - - +
31X VAL* 4.2 17.3 - - + -
46X LEU* 4.4 12.6 - - + -
52X VAL* 5.0 1.1 - - + -
65X VAL* 3.4 29.2 - - + -
66X TRP* 1.3 75.9 - - - +
69X GLY* 1.3 62.2 - - - +
70X ARG* 3.2 7.7 + - - +
80X ALA* 3.3 2.3 - - - -
81X GLN* 2.8 40.2 + - + +
83X PHE* 3.3 27.1 - - + -
108Y LEU* 4.7 4.9 - - + -
112Y ALA* 3.4 24.7 - - + -
118Y VAL* 3.7 20.6 - - + -
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Residues in contact with GLY 69 (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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27X HIS* 6.1 0.4 - - - -
28X PRO 5.4 2.6 + - - -
30X GLN 4.6 6.7 + - - -
67X LEU* 1.3 74.2 - - - +
70X ARG* 1.3 61.3 + - - +
71X HIS* 4.2 0.5 + - - +
77X GLU* 4.2 3.3 - - - +
79X THR* 2.6 40.3 + - - -
80X ALA* 3.7 4.4 + - - -
117Y ALA* 4.1 13.1 + - - +
118Y VAL* 3.8 13.5 - - - +
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Residues in contact with ARG 70 (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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27X HIS* 3.5 16.6 + - - -
30X GLN 5.1 3.8 + - - +
32X ALA* 5.2 1.6 - - + -
34X TYR* 3.8 15.7 + - - -
66X TRP* 3.4 54.4 - - + +
67X LEU 3.2 12.3 - - - +
69X GLY* 1.3 83.0 - - - +
71X HIS* 1.3 59.0 + - - +
72X ASN 4.0 0.2 + - - -
73X LEU* 2.6 52.6 + - + +
74X PHE* 4.9 0.2 - - - +
75X GLU 3.2 21.4 + - - -
76X ASN* 5.0 1.8 - - - +
77X GLU* 3.4 12.0 + - - +
80X ALA* 4.2 9.8 - - + +
141Y TRP* 3.5 20.1 - - + -
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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