Contacts of the helix formed by residues 27 - 40 (chain B) in PDB entry 3P9K
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 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO* 3.8 11.9 - - - +
31A MET* 5.6 0.4 - - - -
128A ASN* 4.1 11.4 + - - +
129A GLN* 2.6 35.4 + - - -
134A MET* 4.1 21.2 - - - -
137A TRP* 4.6 6.1 + - - -
25B SER* 2.8 3.7 + - - -
26B SER* 1.3 77.4 + - - +
28B VAL* 1.3 67.9 + - - +
29B LEU 3.3 0.7 - - - -
30B PRO* 3.3 4.8 - - - +
31B MET* 3.1 29.1 + - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 4.0 15.7 - - + -
312A HIS* 3.7 33.7 - - + +
315A MET* 3.7 18.8 - - + -
316A ILE* 3.8 18.8 - - + -
25B SER* 3.1 16.1 + - - +
27B SER* 1.3 81.2 + - - +
29B LEU* 1.3 57.2 + - - +
32B THR* 2.5 48.6 + - - +
80B LEU* 4.0 17.3 - - + -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.2 20.6 - - + -
26A SER* 4.4 11.7 - - - +
312A HIS* 5.2 2.5 + - - +
26B SER 4.0 5.8 + - - +
28B VAL* 1.3 79.1 - - - +
30B PRO* 1.3 69.1 - - + +
32B THR* 3.7 0.2 - - - -
33B LEU* 2.8 35.8 + - + +
80B LEU* 4.3 7.0 - - + -
81B LEU* 4.1 20.6 - - + -
84B TYR* 3.8 55.4 - - + +
86B VAL* 4.6 6.3 - - + -
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Residues in contact with PRO 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 5.1 0.7 - - - +
26A SER* 3.0 41.3 - - - +
27A SER* 3.7 18.4 - - - +
26B SER 3.3 13.7 - - - +
27B SER* 3.3 18.8 - - - +
29B LEU* 1.3 94.7 - - + +
31B MET* 1.3 60.2 + - + +
33B LEU* 3.8 5.5 - - + +
34B LYS* 2.9 29.6 + - - +
129B GLN* 4.0 20.2 + - + +
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Residues in contact with MET 31 (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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27A SER* 5.4 0.2 - - - -
134A MET* 4.0 21.1 - - + -
137A TRP* 3.5 52.7 - - + -
138A TYR* 3.7 30.5 - - + +
27B SER* 3.1 20.0 + - - +
30B PRO* 1.3 80.6 - - + +
32B THR* 1.3 57.9 + - - +
34B LYS* 3.6 18.0 + - + +
35B ASN* 2.7 35.2 + - - -
129B GLN* 3.9 23.8 - - - +
134B MET* 4.7 7.0 - - - -
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 3.8 6.6 - - - -
140A LEU* 4.9 3.3 - - + +
315A MET* 3.6 21.6 - - + +
28B VAL* 2.5 38.4 + - - +
29B LEU 3.7 1.8 - - - -
31B MET* 1.3 75.3 - - - +
33B LEU* 1.3 66.7 + - - +
35B ASN* 3.2 5.0 + - - +
36B ALA* 2.9 21.1 + - - +
77B ILE* 3.8 31.2 - - + +
80B LEU* 3.9 21.3 - - + -
81B LEU* 4.2 3.6 - - + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.7 52.0 - - + +
24A ALA 4.9 0.2 - - - +
26A SER* 5.1 1.8 - - - +
29B LEU* 2.8 19.8 + - + +
30B PRO* 3.8 4.5 - - + +
32B THR* 1.3 78.1 - - - +
34B LYS* 1.3 62.9 + - - +
36B ALA* 3.2 5.2 + - + +
37B ILE* 3.0 42.8 + - + +
42B LEU* 4.0 26.7 - - + -
81B LEU* 4.1 15.1 - - + +
86B VAL* 4.2 17.3 - - + -
112B LEU* 4.4 7.0 - - + -
125B ALA* 5.3 4.9 - - + -
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP 5.7 0.4 - - - +
138A TYR* 4.7 13.7 - - + +
30B PRO 2.9 18.7 + - - +
31B MET* 3.6 19.3 - - + +
32B THR 3.2 0.2 - - - -
33B LEU* 1.3 77.9 - - - +
35B ASN* 1.3 62.1 + - - +
37B ILE* 3.3 8.6 + - - +
38B GLU* 2.8 64.4 + - - +
125B ALA* 4.5 6.1 - - - +
126B LEU* 4.0 21.7 + - + +
129B GLN* 2.9 48.5 - - + +
130B ASP* 4.0 11.3 + - - +
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Residues in contact with ASN 35 (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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137A TRP* 3.0 31.0 + - - +
138A TYR 4.9 1.2 - - - -
139A TYR 4.9 0.3 + - - -
140A LEU* 3.5 28.3 + - + +
141A LYS* 3.0 27.1 + - + +
31B MET* 2.7 23.8 + - - +
32B THR 3.2 6.3 + - - +
34B LYS* 1.3 82.4 - - - +
36B ALA* 1.3 59.5 + - - +
38B GLU* 3.3 20.0 + - - +
39B LEU* 2.9 39.6 + - + +
77B ILE* 5.6 1.3 - - + -
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Residues in contact with ALA 36 (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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32B THR 2.9 17.2 + - - +
33B LEU* 3.5 9.6 - - + +
35B ASN* 1.3 76.4 - - - +
37B ILE* 1.3 58.6 + - - +
39B LEU* 3.4 1.0 + - - -
40B GLY 3.0 21.5 + - - -
41B LEU* 3.0 39.4 + - + +
42B LEU* 4.1 7.5 + - + -
77B ILE* 4.3 3.7 - - + +
81B LEU* 3.7 26.0 - - + -
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.0 32.1 + - + +
34B LYS* 3.6 7.9 - - - +
36B ALA* 1.3 74.9 - - - +
38B GLU* 1.3 65.2 + - - +
40B GLY* 3.1 14.2 + - - -
42B LEU* 4.0 25.6 - - + +
43B GLU* 5.7 2.6 - - - +
112B LEU* 5.1 8.1 - - + +
122B ALA* 4.1 27.6 - - + -
125B ALA* 3.8 29.2 - - + -
126B LEU* 4.0 20.4 - - + -
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Residues in contact with GLU 38 (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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137A TRP 5.3 0.2 - - - +
138A TYR* 6.1 0.7 - - - -
141A LYS* 3.8 36.9 + - + +
34B LYS* 2.8 43.5 + - - +
35B ASN* 3.3 30.4 + - - +
37B ILE* 1.3 76.6 - - - +
39B LEU* 1.3 61.7 + - - +
40B GLY 3.6 0.2 + - - -
126B LEU* 3.6 20.2 - - + +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 3.7 30.7 - - + +
144A VAL* 4.0 31.2 - - + -
145A LEU* 3.8 30.5 - - + -
35B ASN* 2.9 25.9 + - + +
36B ALA 3.7 4.5 - - - +
37B ILE 3.2 0.2 - - - -
38B GLU* 1.3 78.2 - - - +
40B GLY* 1.3 59.1 + - - +
41B LEU* 3.8 27.8 - - + -
44B ILE* 5.1 0.3 - - - +
62B LEU* 3.3 25.7 - - + +
77B ILE* 4.5 7.2 - - + -
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Residues in contact with GLY 40 (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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36B ALA 3.0 4.8 + - - -
37B ILE* 3.1 13.0 + - - -
38B GLU 3.3 0.2 - - - -
39B LEU* 1.3 79.1 - - - +
41B LEU* 1.3 59.4 + - - +
42B LEU 3.2 2.9 - - - -
43B GLU* 3.0 25.6 + - - +
44B ILE* 2.9 34.7 + - - +
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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