Contacts of the strand formed by residues 29 - 35 (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 TRP 29 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26X SER 3.4 19.0 + - - -
27X HIS* 3.9 22.0 - - + -
28X PRO* 1.3 94.8 - - + +
30X GLN* 1.3 79.4 + - - +
31X VAL* 4.7 0.2 - - - -
45X VAL* 3.3 6.9 - - + -
46X LEU* 2.9 32.0 + - - +
119Y LYS* 3.2 18.6 - - + +
120Y VAL 5.0 2.7 - - - -
121Y LEU* 3.5 45.1 - - + +
137Y GLU* 5.0 9.9 - - - -
139Y SER* 4.1 11.9 - - - -
157Y CYS* 6.4 0.2 - - - -
198Y PRO* 3.2 33.0 - - + -
200Y ILE* 3.5 27.5 - - + +
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Residues in contact with GLN 30 (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* 3.1 22.3 + - + +
28X PRO 3.3 2.3 - - - +
29X TRP* 1.3 84.2 - - + +
31X VAL* 1.3 72.2 + - - +
32X ALA 4.3 0.2 + - - -
43X GLY* 3.9 11.3 - - - -
44X GLY 3.6 13.0 + - - +
66X TRP 4.5 3.1 - - - +
67X LEU* 4.7 1.7 - - - +
69X GLY 4.6 11.6 + - - -
70X ARG 5.1 2.9 + - - +
139Y SER* 2.7 40.6 + - - +
140Y GLY* 4.7 2.6 - - - -
141Y TRP* 3.7 20.8 - - + -
155Y ILE* 3.4 24.5 - - + +
197Y GLY* 4.2 2.3 - - - -
198Y PRO* 3.6 15.3 - - - +
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Residues in contact with VAL 31 (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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29X TRP 3.8 1.1 - - - +
30X GLN* 1.3 85.4 - - - +
32X ALA* 1.3 61.9 + - - +
33X ILE* 3.6 18.6 - - + -
43X GLY* 3.4 3.5 - - - -
44X GLY* 3.0 32.1 + - - -
45X VAL 3.9 5.6 - - - +
46X LEU* 3.6 29.4 - - + +
52X VAL* 3.9 18.6 - - + -
65X VAL* 3.5 31.4 - - + -
66X TRP 3.7 6.1 - - - +
67X LEU* 4.2 11.2 - - + -
141Y TRP* 4.0 4.5 - - - -
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Residues in contact with ALA 32 (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 4.3 0.2 + - - -
31X VAL* 1.3 72.5 - - - +
33X ILE* 1.3 61.2 + - - +
34X TYR* 3.6 25.9 - - + +
40X PHE* 3.8 15.3 - - + -
42X CYS 3.9 3.6 - - - -
65X VAL* 3.6 1.6 - - - -
66X TRP* 2.8 46.4 + - + +
70X ARG* 5.2 1.1 - - + -
73X LEU* 4.5 5.4 - - + -
141Y TRP* 3.9 17.0 - - + -
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Residues in contact with ILE 33 (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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31X VAL* 3.6 15.0 - - + -
32X ALA* 1.3 74.3 - - - +
34X TYR* 1.3 60.9 + - - +
35X HIS* 4.6 6.5 - - - +
40X PHE* 3.9 1.6 - - - -
41X GLN* 2.8 30.2 + - - -
42X CYS* 2.8 29.1 + - + +
43X GLY 3.5 20.9 - - - +
52X VAL* 3.9 10.8 - - + -
54X THR* 3.7 22.9 - - + +
58X CYS* 5.3 2.0 - - + +
63X TYR* 4.0 29.2 - - + -
64X GLU 3.6 5.4 - - - +
65X VAL* 4.6 4.5 - - + -
106Y LEU* 3.8 20.2 - - + -
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Residues in contact with TYR 34 (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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32X ALA* 3.6 27.1 - - + -
33X ILE* 1.3 77.6 - - - +
35X HIS* 1.3 67.5 + - - +
38X SER* 3.8 13.9 - - - -
39X SER 3.3 9.4 - - - +
40X PHE* 3.2 35.2 - + + -
63X TYR* 3.2 8.3 - - - +
64X GLU* 2.9 55.4 + - + +
66X TRP* 3.4 31.0 - + - -
70X ARG* 3.8 12.0 + - - -
73X LEU* 3.5 31.9 - - - +
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Residues in contact with HIS 35 (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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33X ILE* 4.6 3.5 - - + +
34X TYR* 1.3 82.6 - - - +
36X TYR* 1.3 75.4 + - + +
38X SER 3.1 1.6 - - - -
39X SER* 2.9 24.0 + - - +
41X GLN* 3.2 37.7 - - + +
57X HIS 5.4 0.9 - - - -
58X CYS* 2.7 37.7 + - - +
59X LYS 4.3 1.8 - - - -
60X ASN* 3.4 39.8 - - + +
62X ASN 3.6 8.1 - - - -
63X TYR* 3.7 11.2 - + - -
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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