Contacts of the strand formed by residues 32 - 39 (chain A) in PDB entry 2PK9
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 TYR 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LYS* 3.6 28.3 - - - -
24A GLY 3.6 3.8 - - - +
25A LEU* 3.7 35.5 - - + +
30A GLY 3.5 14.6 - - - -
31A VAL* 1.3 82.4 - - - +
33A VAL* 1.3 64.9 + - - +
69A TYR* 4.8 1.2 - - - -
83A GLU* 5.0 0.2 - - - -
84A PHE* 3.4 33.4 + + + +
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Residues in contact with VAL 33 (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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7A PHE* 3.6 35.9 - - + -
23A LYS* 3.5 4.5 - - - +
24A GLY* 2.7 51.4 + - - +
25A LEU* 4.1 1.1 - - - +
26A ASN* 5.8 0.2 - - - +
31A VAL* 4.1 13.5 - - + +
32A TYR* 1.3 79.5 - - - +
34A ALA* 1.3 56.9 + - - +
35A LEU* 4.4 5.8 - - + -
69A TYR* 3.6 31.4 - - + -
81A VAL* 3.8 15.5 - - + -
82A PHE 3.7 6.7 - - - +
84A PHE* 3.6 9.5 - - - +
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Residues in contact with ALA 34 (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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13A LEU* 4.6 3.8 - - + -
21A VAL* 4.4 13.5 - - + -
22A TYR 3.3 9.9 - - - +
23A LYS* 4.5 0.7 - - - +
33A VAL* 1.3 71.7 - - - +
35A LEU* 1.3 63.4 + - - +
36A LYS* 3.6 0.7 + - - +
80A LEU 3.5 1.2 - - - +
81A VAL* 3.8 0.6 - - - -
82A PHE* 2.8 51.5 + - + +
83A GLU 4.8 1.1 - - - +
84A PHE* 3.7 22.5 - - + +
85A MET 5.2 0.9 - - - +
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Residues in contact with LEU 35 (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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7A PHE* 4.0 32.3 - - + -
9A GLN* 4.2 28.0 - - + +
20A THR 3.9 0.2 - - - +
21A VAL* 3.4 3.1 - - - +
22A TYR* 2.7 45.0 + - + +
23A LYS 5.0 0.7 - - - -
24A GLY* 4.2 16.6 - - - +
33A VAL* 3.9 7.8 - - + -
34A ALA* 1.3 71.2 - - - +
36A LYS* 1.3 59.5 + - - +
37A GLU* 3.8 6.9 + - + +
72A ILE* 4.7 1.8 - - + -
79A THR* 4.0 18.4 - - + +
80A LEU 3.8 1.8 - - - -
81A VAL* 3.9 31.0 - - + -
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Residues in contact with LYS 36 (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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18A TYR* 3.5 30.3 - - - -
19A ALA* 3.7 20.4 - - + -
20A THR 4.0 2.5 - - - -
21A VAL* 4.2 17.0 - - + -
34A ALA 3.6 0.6 + - - +
35A LEU* 1.3 70.7 - - - +
37A GLU* 1.3 59.4 + - - +
38A VAL* 3.4 5.2 + - + +
53A GLU* 3.0 29.2 + - - -
78A LEU 3.7 0.2 - - - +
79A THR* 4.2 0.7 - - - -
80A LEU* 2.7 50.3 + - + +
82A PHE* 3.8 24.0 - - + -
151A ASP* 3.8 16.6 + - - +
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Residues in contact with GLU 37 (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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9A GLN* 3.1 24.6 + - - -
19A ALA* 3.2 4.0 - - - -
20A THR* 2.9 68.8 + - + +
22A TYR* 3.3 15.2 - - - -
35A LEU* 4.8 7.9 - - + +
36A LYS* 1.3 70.1 - - - +
38A VAL* 1.3 61.4 + - - +
39A LYS 3.9 0.3 + - - -
77A LYS* 2.7 41.3 + - + -
78A LEU 3.8 4.3 - - - -
79A THR* 3.7 10.1 - - + +
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Residues in contact with VAL 38 (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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18A TYR* 2.0 83.7 - - + +
19A ALA* 4.4 2.5 - - + -
36A LYS* 3.8 6.1 - - + +
37A GLU* 1.3 75.2 - - - +
39A LYS* 1.3 64.5 + - - +
40A LEU* 3.2 6.1 + - - +
47A PRO* 3.6 17.0 - - + -
50A ALA* 4.2 2.5 - - + -
77A LYS* 4.4 2.0 - - - +
78A LEU* 2.8 38.3 + - + +
80A LEU* 3.8 22.7 - - + -
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Residues in contact with LYS 39 (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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15A ASN* 6.1 0.9 - - - +
16A GLY 4.9 7.3 + - - -
17A THR* 3.7 27.4 + - - +
18A TYR 3.2 17.6 + - - +
19A ALA 5.0 0.9 - - - +
20A THR* 4.7 18.2 - - + -
37A GLU 3.9 3.3 + - - +
38A VAL* 1.3 68.0 - - - +
40A LEU* 1.3 58.8 + - - +
42A SER* 5.5 3.0 - - - -
44A GLU* 5.2 2.1 - - - +
47A PRO* 3.3 23.6 - - - +
77A LYS* 5.9 0.7 - - - +
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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