Contacts of the helix formed by residues 32 - 46 (chain A) in PDB entry 6H2U
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 ARG 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TYR* 4.2 5.6 - - - +
30A PRO* 3.2 37.7 + - - +
31A THR* 1.3 74.6 - - - +
33A PRO* 1.3 74.3 - - + +
34A HIS* 4.6 3.4 - - + +
35A ILE* 3.0 18.7 + - + +
36A ALA* 2.9 19.4 + - - +
126A ASN* 5.2 0.2 - - - +
184A TYR* 3.6 33.8 - - + -
185A ASP 2.8 28.2 + - - +
186A LEU* 3.5 1.2 - - - +
187A PRO* 3.3 34.4 - - - +
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Residues in contact with PRO 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.9 10.0 - - + +
13A LEU* 3.9 24.0 - - + +
14A GLN* 3.9 37.2 - - + +
31A THR 3.8 6.1 - - - +
32A ARG* 1.3 86.0 - - + +
34A HIS* 1.3 58.1 + - - +
36A ALA* 3.9 5.7 - - + +
37A ALA* 2.8 33.4 + - - +
64A VAL* 5.0 2.2 - - + -
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Residues in contact with HIS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 6.2 1.6 - - + -
10A GLU* 3.2 33.7 + - - +
32A ARG* 3.3 3.4 - - + +
33A PRO* 1.3 78.8 - - - +
35A ILE* 1.3 71.9 + - + +
37A ALA* 4.1 0.2 - - - +
38A CYS* 3.1 53.4 + - - -
182A LEU* 6.1 4.2 - - + +
183A ARG 6.2 0.2 - - - -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 4.2 9.9 - - + -
32A ARG* 3.0 14.9 + - + +
34A HIS* 1.3 82.6 - - + +
36A ALA* 1.3 66.8 + - - +
38A CYS* 3.9 2.8 - - - +
39A MET* 3.0 28.6 + - - +
156A LEU* 4.0 28.3 - - + -
182A LEU* 3.7 40.5 - - + +
183A ARG 3.6 22.0 - - - +
184A TYR* 3.9 30.5 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.9 11.7 - - + -
31A THR* 3.8 4.5 - - + +
32A ARG 2.9 12.6 + - - +
33A PRO* 3.9 1.6 - - + +
35A ILE* 1.3 77.7 - - - +
37A ALA* 1.3 57.9 + - - +
39A MET* 3.8 0.8 - - - +
40A LEU* 2.9 36.8 + - + +
64A VAL* 3.5 31.6 - - + -
65A LEU* 3.7 25.1 - - + -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.5 12.9 - - + +
9A LEU* 3.8 14.8 - - + +
10A GLU* 3.6 37.0 - - + +
13A LEU* 3.9 3.8 - - + +
33A PRO 2.8 19.2 + - - +
34A HIS 4.1 2.7 - - - +
36A ALA* 1.3 76.8 - - - +
38A CYS* 1.3 57.6 + - - +
41A TYR* 2.8 33.6 + - - +
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Residues in contact with CYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.1 21.5 - - - -
10A GLU* 5.2 0.2 - - - -
34A HIS* 3.1 52.8 + - - +
35A ILE* 4.1 3.1 - - - +
37A ALA* 1.3 78.5 - - - +
39A MET* 1.3 62.7 + - - +
41A TYR* 4.0 1.3 - - - +
42A THR* 2.8 31.8 + - - +
182A LEU* 5.4 13.5 - - + -
204A LEU* 5.4 1.1 - - - -
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.0 21.1 + - + +
36A ALA 3.8 2.9 - - - +
38A CYS* 1.3 77.8 - - - +
40A LEU* 1.3 58.5 - - + +
42A THR* 3.7 2.1 - - - -
43A ILE* 3.0 40.3 + - + +
65A LEU* 4.1 23.3 - - + -
124A ILE* 4.4 8.7 - - + -
125A MET 3.9 20.9 - - - +
154A TYR* 3.8 30.1 - - + +
155A SER* 4.5 0.9 - - - +
156A LEU* 4.1 19.5 - - + -
182A LEU* 5.7 1.9 - - + +
204A LEU* 3.8 41.8 - - + +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.3 3.1 - - + -
13A LEU* 4.3 8.3 - - + -
36A ALA 2.9 28.7 + - - +
37A ALA 4.2 1.3 - - - +
39A MET* 1.3 71.2 - - + +
41A TYR* 1.3 66.0 + - - +
43A ILE* 3.3 12.6 + - + +
44A HIS* 3.0 25.6 + - - +
50A ILE* 4.0 10.8 - - + +
65A LEU* 3.7 26.2 - - + +
68A GLY* 3.5 32.3 - - - -
69A THR* 3.4 22.0 - - - +
72A LEU* 3.8 17.3 - - + +
124A ILE* 4.1 12.3 - - + -
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Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LYS* 2.6 37.9 + - - -
4A VAL 3.8 6.1 - - - -
5A ARG* 4.6 3.9 + - - -
6A LEU* 3.7 49.1 - - + -
9A LEU* 4.2 9.8 - - + +
37A ALA 2.8 20.2 + - - +
38A CYS* 4.0 2.7 - - - +
40A LEU* 1.3 76.8 - - - +
42A THR* 1.3 63.1 + - - +
44A HIS* 4.7 1.6 - - - -
45A ASN* 2.8 64.6 + - + +
72A LEU* 4.8 3.6 - - + -
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A CYS* 2.8 22.8 + - - +
39A MET* 3.7 5.2 - - - -
41A TYR* 1.3 80.3 - - - +
43A ILE* 1.3 65.9 + - - +
45A ASN* 5.2 0.2 - - - -
46A THR* 2.9 44.8 + - + +
47A TYR* 3.4 20.4 + - + -
179A ILE* 4.4 16.6 - - + -
204A LEU* 5.2 4.2 - - + +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.0 32.7 + - + +
40A LEU* 3.7 14.1 - - + +
42A THR* 1.3 77.5 - - + +
44A HIS* 1.3 57.1 + - - +
47A TYR* 3.4 11.8 + - - +
48A ASP 3.0 21.5 + - - -
49A ASP* 3.2 27.4 + - + +
50A ILE* 3.6 24.9 - - + -
122A THR* 4.8 2.0 - - + -
124A ILE* 4.0 14.1 - - + -
154A TYR* 3.6 50.9 - - + -
179A ILE* 5.9 0.7 - - + -
204A LEU* 6.1 0.7 - - + -
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Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LYS* 5.9 3.8 - - + +
4A VAL 6.0 1.3 - - - -
40A LEU 3.0 16.2 + - - +
41A TYR* 3.9 2.5 - - - +
43A ILE* 1.3 78.8 - - - +
45A ASN* 1.3 87.0 + - - +
48A ASP* 3.0 33.8 + - - +
49A ASP 4.5 2.0 - - - +
50A ILE* 4.5 7.5 - - + +
51A GLU* 3.4 44.9 + - + +
72A LEU* 4.1 39.7 + - + +
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Residues in contact with ASN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LYS* 3.9 19.8 - - - +
4A VAL 5.0 0.3 - - - +
41A TYR* 2.8 64.8 + - + +
42A THR* 5.2 0.2 - - - -
44A HIS* 1.3 99.2 + - - +
46A THR* 1.3 62.5 + - - +
48A ASP* 5.0 0.3 + - - +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 2.9 26.3 + - + +
45A ASN* 1.3 82.4 - - - +
47A TYR* 1.3 89.9 + - + +
48A ASP* 3.7 0.8 - - - +
304A EDO 3.3 15.5 + - - +
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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