Contacts of the helix formed by residues 32 - 49 (chain C) in PDB entry 1V8O
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 LEU 32 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.9 9.2 - - + -
31C ILE* 1.3 86.2 - - - +
33C HIS* 1.3 66.2 + - - +
34C LEU* 3.9 8.5 - - + +
35C THR* 2.7 26.6 + - - +
36C ILE* 4.0 0.5 + - - +
70C VAL* 3.7 5.7 - - - +
71C LEU* 4.2 11.9 - - + +
72C GLU 4.7 5.8 - - - +
73C ASP* 5.4 0.2 - - - +
74C PRO* 4.8 0.2 - - + -
94C SER* 3.9 33.7 - - - +
95C TYR* 3.8 33.0 - - + -
98C VAL* 3.6 34.1 - - + -
37D TYR* 4.1 16.4 - - + +
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Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 1.3 74.0 - - - +
34C LEU* 1.3 61.6 + - - +
35C THR 3.3 0.3 + - - -
36C ILE* 3.4 13.0 + - - +
37C TYR* 3.2 21.6 - - - -
70C VAL* 3.6 22.9 + - + +
71C LEU 3.7 18.1 + - - -
72C GLU* 5.4 1.4 - - - -
73C ASP* 3.3 21.2 + - - +
33D HIS* 3.3 61.2 + + + -
37D TYR* 4.6 0.7 - - + -
73D ASP* 2.5 31.8 + - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.4 5.6 - - + -
33C HIS* 1.3 77.3 - - - +
35C THR* 1.3 66.3 + - - +
37C TYR* 3.0 14.8 + - + -
38C GLU* 3.0 51.9 + - + +
91C TYR* 3.5 41.7 - - + +
94C SER* 4.7 1.1 - - - -
95C TYR* 4.3 6.7 - - + +
34D LEU* 5.8 4.0 - - + -
37D TYR* 3.5 49.4 - - + -
91D TYR* 4.9 3.4 - - + +
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Residues in contact with THR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL 3.9 5.8 - - - +
8C ASP 3.8 7.6 - - - +
9C ALA* 3.8 21.8 - - - +
12C LEU* 4.4 11.0 - - + -
31C ILE* 3.3 17.7 - - + +
32C LEU* 2.7 31.1 + - - -
34C LEU* 1.3 76.8 - - - +
36C ILE* 1.3 59.0 + - - +
38C GLU* 3.0 3.6 + - - +
39C ALA* 2.8 33.4 + - + +
65C MSE 4.5 2.0 - - + -
95C TYR* 3.2 24.6 + - - +
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 3.9 22.0 - - + -
32C LEU 4.3 0.4 - - - +
33C HIS* 3.6 14.4 - - - +
34C LEU 3.2 0.4 - - - -
35C THR* 1.3 75.5 - - - +
37C TYR* 1.3 65.5 + - + +
39C ALA* 3.7 1.9 - - - +
40C GLY* 2.8 26.9 + - - -
65C MSE 3.7 23.3 - - + -
70C VAL* 4.7 10.3 - - + -
73D ASP* 3.2 33.9 - - + +
74D PRO* 5.1 9.4 - - + +
76D LEU* 4.1 19.8 - - + +
90D PHE* 4.3 3.6 - - + -
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Residues in contact with TYR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C HIS 3.2 28.9 - - - -
34C LEU* 3.0 12.5 + - + +
36C ILE* 1.3 79.0 - - + +
38C GLU* 1.3 62.1 + - - +
40C GLY* 3.2 0.5 + - - -
41C ASN* 2.8 31.5 + - - +
32D LEU* 4.2 13.9 - - + +
33D HIS* 4.8 0.4 - - + -
34D LEU* 3.7 44.1 + - + -
73D ASP* 3.1 23.7 + - + -
74D PRO* 3.1 29.7 - - + +
79D VAL* 6.1 0.2 - - + -
90D PHE* 3.8 14.4 - + - -
91D TYR* 3.6 19.0 - + + -
94D SER* 3.3 34.5 - - - -
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Residues in contact with GLU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 3.3 22.0 + - + +
34C LEU* 3.0 44.3 + - + +
35C THR 3.5 5.8 - - - +
37C TYR* 1.3 75.4 - - - +
39C ALA* 1.3 64.9 + - - +
41C ASN* 3.2 4.1 + - - +
42C ALA* 2.9 24.0 + - - +
91C TYR* 3.7 18.5 - - + +
92C ASP* 5.6 0.7 - - - +
95C TYR* 2.7 30.7 + - - -
91D TYR* 4.2 13.7 - - - +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 4.2 8.9 - - + +
12C LEU* 4.3 12.3 - - + -
13C TYR* 4.3 8.2 - - + -
35C THR 2.8 19.9 + - - +
36C ILE 3.7 3.6 - - - +
38C GLU* 1.3 71.9 - - - +
40C GLY* 1.3 63.3 + - - +
42C ALA* 3.3 8.4 + - - +
43C LEU 3.2 17.2 + - - -
61C LEU* 3.6 26.3 - - + +
65C MSE 4.2 18.6 - - + -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE 2.8 17.8 + - - -
37C TYR 3.6 1.3 - - - -
38C GLU 3.2 0.2 - - - -
39C ALA* 1.3 77.3 - - - +
41C ASN* 1.3 56.4 + - - +
43C LEU* 3.3 5.2 + - - +
44C TRP* 2.9 27.4 + - - +
61C LEU* 4.5 1.8 - - - -
76D LEU* 3.8 18.3 - - - +
80D MSE 4.4 2.0 - - - +
90D PHE* 3.8 21.7 - - - -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TYR 2.8 20.5 + - - +
38C GLU* 3.7 4.0 - - - +
40C GLY* 1.3 70.2 - - - +
42C ALA* 1.3 67.6 + - - +
44C TRP* 3.2 25.4 + - - +
45C LYS* 3.0 52.3 + - - +
89D THR* 4.7 4.2 - - - -
90D PHE* 3.8 21.0 - - + +
91D TYR* 4.0 28.1 - - + +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 6.3 1.3 - - + -
13C TYR* 4.0 24.2 - - + -
38C GLU 2.9 13.4 + - - +
39C ALA* 3.6 9.9 - - - +
40C GLY 3.3 0.2 - - - -
41C ASN* 1.3 76.6 - - - +
43C LEU* 1.3 62.5 + - - +
45C LYS* 3.1 22.4 + - - +
46C GLU* 3.2 15.2 + - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 3.5 16.1 + - + +
39C ALA 3.2 10.5 + - - +
40C GLY 3.6 7.6 - - - +
42C ALA* 1.3 76.8 - - - +
44C TRP* 1.3 65.6 + - - +
46C GLU* 3.3 13.5 + - + -
47C ALA* 3.1 17.2 + - - +
51C ARG* 4.4 9.2 - - - +
54C TRP* 4.3 7.6 - - - +
57C ALA* 3.9 22.0 - - + +
58C SER* 3.5 41.5 - - - +
61C LEU* 4.0 17.9 - - + -
76D LEU* 5.0 1.8 - - + -
80D MSE 4.5 10.1 - - - -
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Residues in contact with TRP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLY 2.9 14.5 + - - +
41C ASN* 3.4 33.2 - - - +
43C LEU* 1.3 77.4 - - - +
45C LYS* 1.3 81.6 + - + +
47C ALA* 3.1 4.7 + - + +
48C ARG* 2.8 72.7 + - + +
80D MSE 3.1 37.6 - - + -
83D ALA* 3.9 15.1 + - + +
84D VAL* 4.9 3.2 - - + +
87D GLY 6.0 0.7 - - - -
88D LEU 3.4 17.9 + - - -
89D THR* 3.6 31.2 - - + -
90D PHE* 4.1 10.1 - - + -
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Residues in contact with LYS 45 (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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45A LYS* 5.5 9.5 - - - +
41C ASN* 3.0 39.0 + - - +
42C ALA* 3.1 13.2 + - - +
44C TRP* 1.3 93.3 - - + +
46C GLU* 1.3 62.9 + - - +
48C ARG* 3.2 8.8 + - - +
49C LEU* 3.0 32.2 + - + +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 3.4 32.4 + - - +
42C ALA 3.2 15.3 + - - +
43C LEU* 3.3 16.4 - - + +
45C LYS* 1.3 77.2 - - - +
47C ALA* 1.3 65.7 + - - +
49C LEU* 3.3 11.9 + - - +
50C GLY 3.4 17.2 + - - +
51C ARG* 3.6 26.9 + - - +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 4.3 6.6 - - - +
43C LEU* 3.1 8.1 + - - +
44C TRP* 3.1 11.9 + - + +
46C GLU* 1.3 78.4 - - - +
48C ARG* 1.3 66.6 + - - +
50C GLY* 2.9 14.7 + - - -
51C ARG* 3.8 14.7 + - - +
54C TRP* 3.5 36.8 - - + -
80D MSE 4.4 7.9 - - + -
84D VAL* 5.1 3.8 - - + -
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Residues in contact with ARG 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLY 5.8 1.6 + - - -
88A LEU* 5.9 1.6 - - - +
89A THR* 5.7 4.9 - - - +
92A ASP* 4.3 11.3 + - - -
110A ASP* 3.0 35.2 + - - +
111A ARG* 2.6 37.9 + - - +
112A GLU* 3.1 43.7 + - - +
44C TRP* 2.8 61.6 + - + +
45C LYS* 3.2 12.3 + - - +
47C ALA* 1.3 70.8 - - - +
49C LEU* 1.3 59.9 + - + +
50C GLY 2.9 5.2 + - - -
87D GLY* 5.4 5.7 + - - -
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.7 31.6 - - - -
109A GLN* 3.2 26.3 - - + +
110A ASP* 3.7 26.9 - - + +
111A ARG* 3.5 3.6 + - - -
45C LYS* 3.0 21.9 + - + +
46C GLU* 3.6 4.7 - - - +
47C ALA 3.3 0.2 - - - -
48C ARG* 1.3 76.1 - - + +
50C GLY* 1.3 64.3 + - - +
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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