Contacts of the strand formed by residues 39 - 48 (chain A) 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 SER 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.2 2.7 - - - -
35A HIS 2.8 37.2 + - - -
36A TYR 3.1 0.4 - - - -
38A SER* 1.3 80.2 - - - +
40A PHE* 1.3 64.5 + - - +
41A GLN* 3.0 15.9 + - - +
127Y GLN* 5.6 0.2 - - - -
128Y GLU* 3.5 25.6 - - - -
129Y PRO 2.8 23.1 + - - -
130Y GLU* 3.8 10.4 - - - -
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Residues in contact with PHE 40 (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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32A ALA* 3.8 17.3 - - + -
33A ILE 4.0 2.9 - - - -
34A TYR* 3.5 33.3 - + + +
39A SER* 1.3 73.4 + - - +
41A GLN* 1.3 74.2 + - - +
42A CYS 3.4 26.0 - - - -
43A GLY 4.6 0.4 - - - -
73A LEU* 3.8 20.6 - - + -
74A PHE* 6.3 2.5 - - + -
141B TRP* 3.6 42.2 - + + -
151B PHE* 5.1 8.5 - + - -
193B GLY* 3.7 25.6 - - - -
130Y GLU* 5.4 4.7 - - + +
132Y LEU* 3.7 15.4 + - + +
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Residues in contact with GLN 41 (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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33A ILE 3.0 9.7 + - - +
35A HIS* 3.4 43.5 + - + +
39A SER* 3.0 36.9 + - - +
40A PHE* 1.3 83.8 + - - +
42A CYS* 1.3 72.8 + - + +
193B GLY* 3.5 21.5 - - - -
128Y GLU* 4.0 14.1 + - - +
129Y PRO 4.1 4.4 + - - -
132Y LEU* 3.7 32.0 - - - +
162Y LEU* 5.6 0.8 - - - +
164Y GLN* 4.5 11.3 + - - +
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Residues in contact with CYS 42 (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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33A ILE* 2.8 38.1 + - + +
35A HIS* 5.5 0.7 - - - -
40A PHE* 3.4 10.7 - - - -
41A GLN* 1.3 94.1 - - + +
43A GLY* 1.3 66.0 + - - +
54A THR* 4.2 0.9 - - - +
58A CYS* 2.0 55.2 - - + -
193B GLY 3.7 9.4 - - - -
195B SER* 3.4 12.3 - - - +
164Y GLN* 5.0 7.4 - - - -
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Residues in contact with GLY 43 (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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30A GLN* 4.1 9.9 - - - -
31A VAL 3.3 13.2 - - - -
32A ALA* 4.8 0.2 - - - -
33A ILE* 3.4 6.7 - - - +
40A PHE* 5.1 2.5 - - - -
42A CYS* 1.3 76.8 - - - +
44A GLY* 1.3 57.7 + - - -
54A THR* 2.8 21.3 + - - -
140B GLY* 6.3 1.1 - - - -
141B TRP* 5.4 1.6 - - - -
193B GLY 3.8 5.0 + - - -
194B ASP* 4.6 2.0 + - - -
195B SER 2.9 17.6 + - - +
196B GLY 3.6 3.7 - - - -
197B GLY* 4.3 3.8 - - - -
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Residues in contact with GLY 44 (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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30A GLN* 3.9 6.3 + - - +
31A VAL* 3.1 33.6 + - - +
33A ILE* 4.3 3.4 - - - -
43A GLY* 1.3 74.0 - - - -
45A VAL* 1.3 68.9 + - - +
52A VAL* 4.5 0.2 - - - -
53A LEU 3.3 11.9 - - - -
54A THR* 4.2 3.8 - - - -
196B GLY 3.4 8.8 + - - -
197B GLY* 4.1 1.4 - - - +
198B PRO* 4.1 5.4 - - - +
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Residues in contact with VAL 45 (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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29A TRP* 3.4 9.4 - - + +
31A VAL* 3.6 5.1 - - - +
44A GLY* 1.3 78.9 - - - +
46A LEU* 1.3 65.3 + - - +
47A VAL 3.2 4.2 + - - -
52A VAL* 3.3 4.4 - - - +
53A LEU* 2.8 40.8 + - - +
121B LEU* 3.6 40.4 - - + -
196B GLY 4.1 6.5 - - - +
198B PRO* 3.9 24.9 - - + -
209B TRP* 3.3 38.6 - - + -
212B ILE* 4.5 0.2 - - + -
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Residues in contact with LEU 46 (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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28A PRO 5.1 0.7 - - - +
29A TRP* 2.8 18.8 + - - +
31A VAL* 3.6 6.7 - - + +
45A VAL* 1.3 72.5 - - - +
47A VAL* 1.3 58.3 + - - +
48A ASN 3.4 23.6 - - - +
49A PRO* 4.4 8.1 - - + +
51A TRP 3.7 7.4 - - - +
52A VAL* 4.1 10.8 - - + -
67A LEU* 3.7 20.9 - - + -
108B LEU* 4.5 1.8 - - + -
112B ALA* 4.4 1.8 - - + -
114B ILE* 3.9 19.1 - - + -
118B VAL* 3.8 27.6 - - + -
119B LYS 3.5 20.4 - - - +
120B VAL* 3.3 6.5 - - + -
121B LEU 3.1 24.9 + - - +
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Residues in contact with VAL 47 (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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45A VAL 3.2 1.9 + - - +
46A LEU* 1.3 74.8 - - - +
48A ASN* 1.3 61.3 + - - +
51A TRP* 3.0 37.3 + - + +
53A LEU* 4.0 14.4 - - + +
105B LEU* 4.1 15.9 - - + -
120B VAL* 3.4 16.2 - - - +
121B LEU 4.2 4.2 - - - +
123B LEU* 3.7 15.9 - - + +
209B TRP* 3.5 37.9 - - + -
238B ILE* 5.6 3.1 - - + -
242B ILE* 4.4 10.2 - - + +
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Residues in contact with ASN 48 (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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46A LEU* 3.4 7.6 - - - +
47A VAL* 1.3 80.4 - - + +
49A PRO* 1.3 72.0 - - - +
50A LYS* 2.9 37.3 - - - +
51A TRP* 2.7 56.3 + - + +
120B VAL* 3.8 6.6 - - - +
242B ILE* 4.9 11.3 - - + +
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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