Contacts of the helix formed by residues 31 - 52 (chain B) 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 SER 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B CYS* 1.3 73.6 - - - +
32B ARG* 1.3 58.8 + - - +
33B THR* 3.2 18.4 + - - -
34B ASP* 2.9 45.3 + - - +
35B LEU 3.3 4.2 + - - -
92B HIS* 4.8 0.4 - - - -
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B CYS 3.2 3.9 + - - -
31B SER* 1.3 68.3 - - - +
33B THR* 1.3 60.3 + - - +
34B ASP 3.4 0.2 - - - -
35B LEU* 4.0 8.5 - - + +
36B VAL* 3.3 26.9 + - - +
85B THR* 3.3 44.7 + - - +
86B LYS* 4.1 16.8 + - - +
89B SER* 4.2 15.8 + - - +
90B LEU 3.5 19.5 + - - -
91B GLU* 5.3 1.4 - - - +
92B HIS* 3.6 31.0 + - + +
95B LEU* 3.7 16.4 - - + -
86D LYS* 4.1 36.5 + - - +
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 3.1 9.9 + - - -
32B ARG* 1.3 76.4 - - - +
34B ASP* 1.3 69.8 + - - +
35B LEU 3.3 0.2 - - - -
36B VAL* 3.2 5.9 + - - +
37B VAL* 2.9 37.9 + - + +
78B PHE* 5.0 4.7 - - + -
82B ILE* 5.2 6.8 - - + +
86B LYS* 4.3 18.1 + - - +
239B ARG* 4.7 19.3 - - - +
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Residues in contact with ASP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.8 7.3 - - - +
23B LEU* 3.9 19.7 - - + +
30B CYS* 4.3 2.7 - - - -
31B SER* 2.9 35.4 + - - +
33B THR* 1.3 81.0 - - - +
35B LEU* 1.3 55.1 + - - +
37B VAL* 3.2 5.2 + - - +
38B LEU* 2.8 33.9 + - + +
243B TYR* 2.7 42.7 + - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 4.1 9.0 - - + +
30B CYS* 4.1 14.4 - - - -
31B SER 3.3 3.8 + - - +
32B ARG* 4.4 2.2 - - - -
33B THR 3.3 0.6 - - - -
34B ASP* 1.3 76.2 - - - +
36B VAL* 1.3 58.5 + - - +
38B LEU* 3.1 8.6 + - + -
39B ILE* 2.8 44.2 + - + +
92B HIS* 3.8 37.7 - - + +
95B LEU* 4.1 24.9 - - + -
96B MET* 4.2 17.3 - - + -
221B TYR* 3.7 36.1 - - + -
224B ILE* 5.2 2.2 - - + -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG 3.3 18.5 + - - +
33B THR 3.2 6.1 + - - +
35B LEU* 1.3 77.8 - - - +
37B VAL* 1.3 56.6 + - - +
40B SER* 2.7 32.6 + - - -
78B PHE* 3.4 6.8 - - + -
81B PHE* 3.7 27.1 - - + -
82B ILE* 3.4 43.5 - - + +
85B THR* 3.4 24.9 - - + +
95B LEU* 4.1 13.9 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 2.9 26.5 + - + +
34B ASP* 3.2 7.8 + - - +
36B VAL* 1.3 74.8 - - - +
38B LEU* 1.3 67.8 + - - +
40B SER* 3.9 0.9 - - - -
41B ARG* 3.0 45.5 + - + +
78B PHE* 3.5 28.3 - - + -
238B SER* 5.6 2.7 - - - -
239B ARG* 4.2 24.5 - - + +
243B TYR* 3.5 31.9 - - + +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.9 16.2 - - + -
34B ASP 2.8 22.6 + - - +
35B LEU* 3.7 7.2 - - + +
37B VAL* 1.3 77.9 - - - +
39B ILE* 1.3 61.3 + - - +
41B ARG* 3.4 7.4 - - - +
42B MET* 3.1 18.7 + - - +
221B TYR* 4.5 9.2 - - + -
224B ILE* 3.4 41.6 - - + +
225B VAL* 3.8 24.2 - - + -
228B VAL* 3.5 14.0 - - - +
229B GLY* 4.1 11.7 - - - -
243B TYR* 4.0 26.9 - - + -
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 2.8 27.7 + - + +
38B LEU* 1.3 70.6 - - - +
40B SER* 1.3 55.0 + - - +
42B MET* 2.9 8.9 + - - +
43B LEU* 2.7 43.8 + - + +
81B PHE* 3.7 25.1 - - + -
95B LEU* 3.2 46.2 - - + +
96B MET* 4.3 9.9 - - - -
98B SER* 5.9 0.2 - - - -
99B LEU* 3.8 33.4 - - + +
123B LEU* 5.9 0.7 - - + -
224B ILE* 4.2 15.9 - - + -
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL 2.7 23.1 + - - -
37B VAL 3.9 3.1 - - - -
39B ILE* 1.3 77.2 - - - +
41B ARG* 1.3 62.6 + - - +
43B LEU* 3.2 9.7 + - - +
44B VAL* 3.0 28.5 + - - +
77B ILE* 4.1 8.0 - - - +
78B PHE* 3.3 41.5 + - - -
81B PHE* 3.6 12.9 - - - +
235B PRO* 4.6 3.8 - - - -
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.0 39.0 + - + +
38B LEU* 3.4 8.3 - - - +
40B SER* 1.3 77.1 - - - +
42B MET* 1.3 63.0 + - - +
44B VAL* 3.4 4.2 + - - +
45B SER* 3.1 22.9 + - - -
228B VAL* 3.4 28.2 + - + +
229B GLY 3.3 9.9 + - - -
230B SER 3.1 22.1 + - - -
231B PHE* 3.5 17.4 + - - -
233B ALA* 4.6 3.9 - - + +
235B PRO* 3.6 35.0 + - + +
238B SER* 6.2 2.4 - - - -
239B ARG 2.8 29.3 + - - +
241B VAL* 3.0 25.3 + - - +
243B TYR* 3.6 12.7 - - - -
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Residues in contact with MET 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU 3.1 9.2 + - - +
39B ILE 2.9 11.8 + - - +
41B ARG* 1.3 75.3 - - - +
43B LEU* 1.3 57.4 + - - +
45B SER* 3.3 5.9 + - - -
46B LEU* 3.0 48.2 + - + +
99B LEU* 3.9 18.4 - - + -
223B ARG* 4.5 1.8 - - + +
224B ILE* 3.6 33.4 - - + -
227B LEU* 3.5 45.8 - - + -
228B VAL* 3.6 21.4 - - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 2.7 25.7 + - + +
40B SER* 3.4 11.9 - - - +
41B ARG 3.2 0.2 - - - -
42B MET* 1.3 74.5 - - + +
44B VAL* 1.3 56.9 + - - +
46B LEU* 3.3 7.0 + - + +
47B ILE* 2.9 34.9 + - + +
77B ILE* 3.9 32.5 - - + -
81B PHE* 5.5 1.6 - - + -
99B LEU* 3.7 21.1 - - + -
102B ILE* 3.3 30.1 - - + -
114B LEU* 3.9 19.7 - - + +
119B ALA* 5.5 0.9 - - + -
122B PHE* 6.0 1.1 - - + -
123B LEU* 4.4 18.8 - - + -
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B SER 3.0 7.0 + - - +
41B ARG 3.6 3.1 - - - +
43B LEU* 1.3 72.5 - - - +
45B SER* 1.3 62.5 + - - +
47B ILE* 3.6 16.9 - - + +
48B ALA* 2.9 28.4 + - - +
77B ILE* 3.2 33.7 - - + -
234B SER* 3.7 14.3 - - - -
235B PRO* 3.4 43.5 - - + -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG 3.1 12.8 + - - -
42B MET* 3.4 14.4 - - - -
43B LEU 3.2 0.2 - - - -
44B VAL* 1.3 77.4 - - - +
46B LEU* 1.3 64.9 + - - +
48B ALA* 3.5 4.8 + - - +
49B ILE* 3.1 40.2 + - - +
228B VAL* 4.1 18.1 - - - +
233B ALA* 4.1 19.3 + - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MET* 3.0 38.4 + - + +
43B LEU* 3.5 8.5 - - + +
45B SER* 1.3 75.9 - - - +
47B ILE* 1.3 57.2 + - - +
49B ILE* 3.2 10.2 + - + -
50B ASN* 2.8 52.7 + - - +
99B LEU* 6.0 1.6 - - + -
102B ILE* 4.0 20.9 - - + -
103B ASP* 5.3 4.0 - - - +
106B GLN* 5.1 3.8 - - - +
114B LEU* 4.0 22.4 - - + -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 2.9 29.1 + - + +
44B VAL* 3.7 18.8 - - + +
45B SER 3.3 0.2 - - - -
46B LEU* 1.3 76.7 - - - +
48B ALA* 1.3 61.9 + - - +
51B GLU* 3.3 28.6 + - - +
77B ILE* 5.4 3.8 - - + -
114B LEU* 4.1 13.9 - - + -
115B ASN* 3.8 18.2 - - - +
116B SER* 3.4 34.5 - - - +
119B ALA* 3.7 28.3 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL 2.9 18.1 + - - +
45B SER* 3.7 7.0 - - - +
46B LEU 3.2 0.2 - - - -
47B ILE* 1.3 74.9 - - - +
49B ILE* 1.3 58.1 + - + +
51B GLU* 3.4 2.6 + - - +
52B ASN* 2.8 40.1 + - + +
234B SER* 4.9 10.1 - - - +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 3.1 28.2 + - - +
46B LEU* 4.0 10.1 - - + +
48B ALA* 1.3 80.0 - - + +
50B ASN* 1.3 67.1 + - - +
51B GLU 3.0 1.6 + - - -
52B ASN* 3.4 6.2 + - - +
53B SER* 3.2 24.1 - - - -
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Residues in contact with ASN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 2.8 36.5 + - - +
47B ILE 4.4 1.1 - - - +
49B ILE* 1.3 75.7 - - - +
51B GLU* 1.3 60.6 + - + +
53B SER* 4.2 11.7 + - - +
106B GLN* 3.3 22.9 + - - +
113B THR* 3.6 19.7 - - + +
114B LEU* 3.0 28.3 + - - +
115B ASN* 5.1 0.7 - - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.3 21.2 + - - +
48B ALA* 3.4 2.9 + - - +
49B ILE 3.0 0.6 - - - -
50B ASN* 1.3 76.2 - - - +
52B ASN* 1.3 53.2 + - - +
53B SER 2.4 30.7 + - - +
115B ASN* 3.1 36.2 - - + +
116B SER* 2.8 29.0 + - - -
117B LEU* 4.0 6.2 - - - +
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Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 2.8 22.5 + - + +
49B ILE* 3.6 4.5 - - - +
51B GLU* 1.3 67.9 - - - +
53B SER* 1.3 60.1 + - - +
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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
------------------------------------------------------------
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