Contacts of the helix formed by residues 42 - 62 (chain C) in PDB entry 2V32
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 THR 42 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ARG* 2.5 38.0 + - + -
40C ASP 3.2 9.8 - - - +
41C PHE* 1.3 84.4 - - - +
43C PRO* 1.4 62.7 - - - +
44C VAL 3.7 0.7 - - - -
45C SER* 3.3 5.7 + - - -
46C THR* 2.6 37.9 + - - -
80C TRP* 4.4 0.2 - - - +
1222C BEZ 3.2 35.4 + - + -
187D PRO* 3.9 15.9 - - + -
212D TYR* 3.7 1.8 - - - -
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Residues in contact with PRO 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR* 1.4 80.3 - - - +
44C VAL* 1.3 64.0 + - - +
46C THR* 3.1 5.2 + - - -
47C THR* 3.0 24.9 + - - +
1222C BEZ 3.3 20.0 - - - +
184D MET* 3.6 30.7 - - + -
185D VAL 3.7 20.6 - - - +
187D PRO* 4.0 13.7 - - + -
212D TYR* 3.5 28.9 - - + +
213D LEU* 3.9 12.1 - - + +
214D ARG 4.5 0.4 - - - +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO* 1.3 74.6 - - - +
45C SER* 1.3 63.5 + - - +
47C THR* 3.0 23.0 + - - -
48C GLU* 3.1 10.1 + - + +
128C ARG* 3.7 17.3 - - - +
147C ALA 4.8 0.4 - - - +
150C GLY* 3.5 20.0 - - - +
1222C BEZ 3.1 20.5 + - - +
172D ALA* 3.5 19.5 - - + -
173D THR 3.3 30.1 - - - +
174D PRO* 3.9 4.7 - - + -
184D MET* 3.5 21.3 - - + +
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C HIS* 3.4 23.1 - - - +
38C PRO* 3.6 5.4 - - - +
39C ARG 3.7 8.7 + - - -
42C THR* 3.3 25.1 + - - -
43C PRO 3.3 0.4 - - - -
44C VAL* 1.3 75.7 - - - +
46C THR* 1.3 63.7 + - - +
48C GLU* 3.3 4.1 + - - +
49C LEU* 3.0 29.5 + - - +
80C TRP* 3.8 5.2 - - - -
128C ARG* 2.9 25.8 + - - +
1222C BEZ 2.9 6.3 + - - -
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR 2.6 23.5 + - - -
43C PRO 3.1 5.1 + - - -
45C SER* 1.3 77.8 - - - +
47C THR* 1.4 55.8 + - - +
49C LEU* 3.4 0.9 + - - +
50C GLY* 2.9 27.7 + - - -
80C TRP* 2.9 29.4 + - - +
83C ASP* 4.2 6.7 - - + +
84C VAL* 4.0 23.5 - - - +
87C LEU* 3.9 17.6 - - + +
206D VAL* 5.9 0.7 - - + -
212D TYR* 3.4 19.6 - - + +
213D LEU* 4.5 6.3 - - + -
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO 3.0 15.2 + - - +
44C VAL 3.0 11.8 + - - -
46C THR* 1.4 75.5 - - - +
48C GLU* 1.3 55.8 + - - +
50C GLY* 3.4 0.7 + - - -
51C ARG* 2.9 29.5 + - - +
87C LEU* 3.9 21.1 - - + -
174D PRO* 3.4 18.9 - - + +
175D ALA* 2.9 32.4 + - - +
184D MET* 4.4 13.2 - - + -
213D LEU* 4.7 0.7 - - + -
215D TYR* 4.6 7.4 - - + +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C HIS* 4.6 0.7 - - - +
44C VAL* 3.1 18.5 + - + +
45C SER* 3.6 6.9 - - - +
47C THR* 1.3 74.6 + - - +
49C LEU* 1.3 69.6 + - + +
50C GLY 3.0 1.6 - - - -
51C ARG* 3.2 5.0 + - - +
52C VAL* 3.1 25.7 + - - +
128C ARG* 3.0 26.8 + - - -
150C GLY* 3.2 5.5 - - - -
151C ARG* 2.6 66.5 + - - +
153C PHE* 3.9 11.7 - - + -
175D ALA* 3.8 21.1 - - + -
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 3.8 20.6 - - + -
37C HIS* 3.7 32.3 - - + +
45C SER 3.0 22.6 + - - +
48C GLU* 1.3 82.1 - - + +
50C GLY* 1.3 61.7 + - - +
52C VAL* 3.4 5.1 + - - -
53C ILE* 3.2 16.5 + - - +
68C ALA* 4.2 4.0 - - + -
80C TRP* 3.6 28.0 - - + -
84C VAL* 3.7 18.2 - - + -
94C MET* 4.7 0.9 - - + -
96C TYR* 2.7 43.4 + - + +
98C ILE* 4.1 11.2 - - + -
151C ARG* 5.1 0.2 - - - +
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Residues in contact with GLY 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR 2.9 18.0 + - - -
47C THR* 3.7 2.2 - - - -
49C LEU* 1.3 76.1 - - - +
51C ARG* 1.3 63.2 + - - +
53C ILE* 3.2 7.1 + - - +
54C GLN* 3.2 20.4 + - - +
84C VAL* 3.8 13.8 - - - +
87C LEU* 5.1 2.0 - - - -
88C SER* 3.4 25.1 - - - -
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Residues in contact with ARG 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLY 3.1 29.5 + - - -
181A ASP* 4.9 3.4 + - - +
217A PRO* 5.6 2.4 - - - +
47C THR 2.9 17.5 + - - +
48C GLU 3.4 7.4 - - - +
50C GLY* 1.3 74.1 - - - +
52C VAL* 1.3 63.5 + - - +
54C GLN* 2.9 42.3 + - - +
55C LEU* 3.1 57.6 + - + +
153C PHE* 4.2 13.9 - - + +
154C SER* 4.3 13.3 + - - -
175D ALA* 4.2 8.1 - - + -
176D ASP* 3.3 29.4 + - - +
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 4.0 16.2 - - + -
48C GLU 3.1 18.1 + - - +
49C LEU 3.7 7.6 - - - +
50C GLY 3.2 0.4 - - - -
51C ARG* 1.3 74.3 - - - +
53C ILE* 1.3 66.1 + - - +
55C LEU* 3.1 7.9 + - - +
56C GLU* 3.0 22.3 + - - +
59C PHE* 4.9 4.7 - - + -
66C LEU* 3.7 31.2 - - + -
96C TYR* 3.4 24.2 - - + +
153C PHE* 3.8 35.0 - - + -
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Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU 3.2 13.1 + - - +
50C GLY 3.2 9.3 + - - +
52C VAL* 1.3 75.9 - - - +
54C GLN* 1.3 61.4 + - - +
56C GLU* 3.0 26.8 + - + +
84C VAL* 3.8 14.8 - - + -
85C LYS* 4.1 20.9 - - + -
88C SER* 3.6 16.4 - - - +
90C VAL* 3.7 25.4 - - + +
93C ASP 5.5 0.9 - - - +
94C MET* 3.6 26.2 - - - -
95C PRO* 3.7 25.1 - - + -
96C TYR* 4.0 6.3 - - + +
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Residues in contact with GLN 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PRO* 3.6 33.2 - - - +
50C GLY 3.2 10.4 + - - +
51C ARG* 2.9 46.3 + - - +
52C VAL 3.2 0.2 - - - -
53C ILE* 1.3 80.0 - - - +
55C LEU* 1.3 58.9 + - - +
56C GLU 3.2 0.7 + - - -
57C GLY 4.9 1.6 + - - -
58C ASP* 4.4 4.3 - - - +
87C LEU 4.3 3.2 + - - -
88C SER* 3.0 34.6 + - - +
90C VAL* 4.2 12.8 - - + -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLY* 5.4 3.8 - - - +
51C ARG* 3.1 52.9 + - - +
52C VAL* 3.1 4.2 + - - +
54C GLN* 1.3 77.0 - - - +
56C GLU* 1.3 65.3 + - - +
57C GLY 3.3 3.1 - - - -
58C ASP* 3.2 31.0 + - + +
59C PHE* 3.1 29.1 + - + -
153C PHE* 3.6 39.5 - - + +
154C SER* 4.9 2.5 - - - +
157C LEU* 4.1 14.6 - - + -
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL 3.0 10.7 + - - +
53C ILE* 3.0 21.1 + - + +
54C GLN 3.2 1.2 - - - -
55C LEU* 1.3 78.1 - - - +
57C GLY* 1.3 69.9 + - - +
59C PHE* 3.2 9.3 + - - +
60C LYS* 2.9 43.2 + - - +
66C LEU* 4.6 11.1 - - + +
95C PRO* 3.7 36.6 - - + +
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLN 4.9 1.6 + - - -
55C LEU 3.3 0.4 - - - -
56C GLU* 1.3 88.8 + - - +
58C ASP* 1.3 55.4 + - - +
60C LYS* 3.5 6.6 - - - +
61C LYS* 2.8 37.2 + - - +
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Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLN 4.4 3.6 - - - +
55C LEU* 3.3 32.8 - - - +
57C GLY* 1.3 76.5 - - - +
59C PHE* 1.3 61.1 + - - +
61C LYS* 3.6 23.8 + - - +
62C ARG* 2.7 42.2 + - - +
157C LEU* 3.8 21.3 - - + -
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Residues in contact with PHE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 4.6 2.9 - - + -
52C VAL* 4.9 7.0 - - + -
55C LEU* 3.1 41.7 + - + -
56C GLU 3.2 7.8 + - - +
58C ASP* 1.3 75.0 - - - +
60C LYS* 1.3 63.4 + - - +
62C ARG* 3.1 14.7 + - - +
64C VAL* 3.1 45.4 + - + +
66C LEU* 3.7 37.5 - - + -
153C PHE* 4.6 13.5 - + + -
156C ILE* 4.1 17.7 - - + -
157C LEU* 3.5 25.6 - - + -
160C ILE* 3.5 31.2 - - + -
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLU* 2.9 33.2 + - - +
57C GLY* 3.3 9.8 + - - +
59C PHE* 1.3 75.7 - - - +
61C LYS* 1.3 63.5 + - - +
63C GLY* 3.0 14.7 + - - +
64C VAL 4.3 4.9 + - - +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLY 2.8 19.4 + - - +
58C ASP* 3.6 24.3 + - - +
59C PHE 3.4 0.2 - - - -
60C LYS* 1.3 72.4 - - - +
62C ARG* 1.3 90.8 + - + +
63C GLY 3.4 0.6 + - - -
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TRP* 5.0 0.5 - - - -
58C ASP* 2.7 45.2 + - - +
59C PHE* 3.1 9.8 + - - +
61C LYS* 1.3 111.2 - - + +
63C GLY* 1.3 61.4 + - - +
64C VAL* 3.4 8.7 + - + -
157C LEU* 4.1 26.9 + - - +
160C ILE* 4.2 12.8 - - - -
161C ASP* 2.8 40.7 + - - +
164C GLN* 2.8 40.8 + - - +
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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
------------------------------------------------------------
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