Contacts of the helix formed by residues 43 - 56 (chain r) in PDB entry 6QX2
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 LYS 43 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33r ARG 3.4 24.5 - - - +
34r ALA* 3.4 24.1 + - - +
35r LEU 4.1 2.9 - - - -
36r PRO* 4.1 18.4 - - + -
41r GLY 4.2 1.0 + - - +
42r LEU* 1.3 73.3 - - - +
44r PRO* 1.4 72.1 - - - +
45r VAL* 4.4 4.7 - - + +
46r HIS* 3.1 29.9 + - + +
47r ARG* 3.1 12.4 + - - +
172r ALA* 5.4 4.7 - - - +
173r SER 2.7 32.1 + - - +
174r GLY* 3.8 3.8 - - - -
5v G 3.4 5.1 + - - -
6v T 3.1 42.7 + - - +
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Residues in contact with PRO 44 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31r VAL 5.1 1.8 - - - +
32r ALA* 3.6 36.6 - - + +
33r ARG* 4.0 10.3 - - - +
35r LEU 4.4 7.9 - - - +
42r LEU 4.5 0.7 - - - +
43r LYS* 1.4 84.9 - - + +
45r VAL* 1.3 63.2 + - - +
47r ARG* 3.2 19.6 + - - +
48r ARG* 2.9 54.8 + - + +
338r LEU* 6.1 1.1 - - + -
7v A 4.6 5.6 - - - +
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Residues in contact with VAL 45 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43r LYS* 4.4 4.4 - - + +
44r PRO* 1.3 78.6 - - - +
46r HIS* 1.3 71.5 + - + +
48r ARG* 3.6 2.0 + - - +
49r ILE* 3.2 44.7 + - + +
74r VAL* 5.9 0.2 - - + -
79r HIS* 3.4 40.9 - - + +
85r SER 4.3 0.4 - - - +
86r ILE* 4.1 12.8 - - + -
89r ALA* 4.0 14.6 - - + -
6v T 3.8 34.3 - - - +
7v A 3.6 7.7 + - - +
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Residues in contact with HIS 46 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41r GLY 5.7 0.2 + - - -
42r LEU* 4.0 20.2 - - + +
43r LYS* 3.1 37.4 + - + +
45r VAL* 1.3 75.2 - - + +
47r ARG* 1.3 65.5 + - - +
49r ILE* 3.2 4.7 + - - +
50r LEU* 3.0 29.6 + - - +
89r ALA* 3.9 21.7 + - + +
92r ARG* 4.5 2.2 + - - -
93r MET* 3.9 28.9 - - + +
99r TYR* 3.9 18.0 + - - -
6v T 3.1 46.4 + - - -
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Residues in contact with ARG 47 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37r ASP* 3.6 13.7 - - - +
40r ASP* 2.9 31.7 + - - -
42r LEU* 3.0 36.6 + - + +
43r LYS 3.1 3.3 + - - +
44r PRO* 3.5 29.7 - - + +
46r HIS* 1.3 78.8 - - - +
48r ARG* 1.3 58.1 + - + +
50r LEU* 3.3 4.1 + - - +
51r TYR* 2.9 30.8 + - - +
157r PRO* 3.3 29.2 - - + +
158r SER 3.6 13.1 + - - -
159r VAL* 3.4 16.0 - - - +
160r LEU* 3.7 20.9 - - + +
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Residues in contact with ARG 48 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32r ALA* 5.8 2.4 + - - +
44r PRO* 2.9 32.3 + - - +
45r VAL 3.9 4.3 - - - +
47r ARG* 1.3 74.4 - - + +
49r ILE* 1.3 62.0 - - - +
51r TYR* 3.9 5.8 - - - +
52r GLY* 2.9 26.2 + - - -
74r VAL* 3.9 14.2 - - + +
78r TYR* 3.3 42.6 + - + -
79r HIS* 3.0 39.3 + - + +
80r PRO* 4.5 5.8 - - - +
81r HIS* 4.9 4.0 + - - -
147r ILE* 6.1 1.0 - - - +
150r TYR* 6.3 0.4 - - - +
156r GLU* 2.7 39.0 + - + +
157r PRO* 6.3 1.3 - - + -
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Residues in contact with ILE 49 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45r VAL* 3.2 28.9 + - + +
46r HIS 3.2 5.6 + - - +
48r ARG* 1.3 74.8 - - - +
50r LEU* 1.3 58.7 + - - +
52r GLY* 3.2 2.9 + - - -
53r LEU* 2.9 41.4 + - + +
70r ILE* 5.0 5.2 - - + -
74r VAL* 3.9 14.2 - - + +
86r ILE* 3.5 41.1 - - + +
89r ALA* 4.1 2.7 - - + -
90r MET* 3.9 28.7 - - + +
93r MET* 3.6 27.8 - - + -
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Residues in contact with LEU 50 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42r LEU* 4.1 15.5 - - + -
46r HIS 3.0 17.0 + - - +
47r ARG 3.9 3.6 - - - +
49r ILE* 1.3 74.4 - - - +
51r TYR* 1.3 62.0 + - - +
53r LEU* 3.4 19.2 + - + +
54r ASN* 3.2 21.5 + - - +
93r MET* 4.1 18.2 - - + -
103r LEU* 3.9 34.5 - - + +
104r VAL* 4.2 3.1 - - + -
132r THR* 4.0 16.6 - - + -
135r LEU* 3.6 30.7 - - + -
136r LEU* 3.7 9.3 - - + +
160r LEU* 4.3 11.7 - - + -
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Residues in contact with TYR 51 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47r ARG 2.9 18.4 + - - +
48r ARG* 3.9 4.0 - - - +
50r LEU* 1.3 74.0 - - - +
52r GLY* 1.3 59.7 + - - +
54r ASN* 3.2 9.2 + - - +
55r GLU* 2.9 69.0 + - + +
78r TYR* 3.6 27.6 - + - -
136r LEU* 4.4 3.8 - - - +
139r ILE* 3.7 17.9 - - + -
140r ASN* 5.8 1.2 + - - -
146r PHE* 3.6 24.4 - + - -
155r ARG* 3.6 18.7 + - - +
156r GLU* 4.8 0.2 - - + -
157r PRO* 3.4 42.4 - - + -
160r LEU* 5.0 2.5 - - + -
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Residues in contact with GLY 52 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48r ARG 2.9 16.5 + - - -
49r ILE 3.5 4.3 - - - -
51r TYR* 1.3 73.8 - - - +
53r LEU* 1.3 64.2 + - - +
55r GLU* 3.5 3.0 + - - +
56r GLN* 3.2 29.5 + - - +
58r MET* 5.5 0.2 - - - +
70r ILE* 5.8 2.2 - - - -
73r ASP* 4.1 9.6 - - - -
74r VAL* 4.4 5.6 - - - -
78r TYR* 3.9 18.6 - - - -
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Residues in contact with LEU 53 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49r ILE* 2.9 25.8 + - + +
50r LEU* 3.5 28.7 - - + +
51r TYR 3.3 0.2 - - - -
52r GLY* 1.3 75.4 - - - +
54r ASN* 1.3 58.3 + - - +
57r GLY 3.3 3.3 + - - -
58r MET* 2.8 51.1 + - + +
70r ILE* 3.7 39.0 - - + +
74r VAL* 5.5 0.2 - - - +
90r MET* 5.4 2.2 - - + -
104r VAL* 4.4 15.0 - - + -
126r ALA* 5.4 0.4 - - + -
127r ARG* 4.4 10.8 - - - +
128r MET* 3.7 30.9 - - + +
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Residues in contact with ASN 54 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50r LEU 3.2 10.7 + - - +
51r TYR* 3.5 11.4 - - - +
52r GLY 3.1 0.2 - - - -
53r LEU* 1.3 77.9 - - - +
55r GLU* 1.3 72.3 + - - +
57r GLY* 3.1 17.7 + - - -
59r THR* 5.1 3.3 - - - +
128r MET* 3.2 22.9 - - + +
133r LEU* 5.5 2.1 - - - +
136r LEU* 3.7 22.8 - - + +
139r ILE* 3.8 24.9 - - - +
140r ASN* 5.0 4.6 - - - +
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Residues in contact with GLU 55 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51r TYR* 2.9 65.4 + - + +
52r GLY 4.0 3.4 - - - +
53r LEU 3.4 0.2 - - - -
54r ASN* 1.3 86.3 + - - +
56r GLN* 1.3 74.6 + - - +
57r GLY 3.3 2.2 + - - -
78r TYR* 3.6 12.6 - - - +
140r ASN* 5.0 9.8 + - - +
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Residues in contact with GLN 56 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52r GLY 3.2 16.7 + - - +
54r ASN 3.3 0.2 - - - -
55r GLU* 1.3 92.0 + - - +
57r GLY* 1.3 64.9 + - - +
58r MET* 2.9 40.1 + - + +
73r ASP* 3.5 24.2 + - + +
77r LYS* 3.4 24.3 + - - +
78r TYR* 5.2 0.2 + - - -
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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