Contacts of the helix formed by residues 43 - 56 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ARG 3.5 24.5 - - - +
34J ALA* 3.4 24.7 + - - +
35J LEU 4.1 2.9 - - - -
36J PRO* 4.1 18.2 - - + -
41J GLY 4.2 0.8 + - - +
42J LEU* 1.3 74.6 - - - +
44J PRO* 1.3 71.5 - - + +
45J VAL* 4.5 5.6 - - + +
46J HIS* 3.1 35.7 + - + +
47J ARG* 3.1 12.9 + - - +
92J ARG* 6.1 0.2 - - - +
172J ALA* 5.4 5.2 - - - +
173J SER 2.7 33.6 + - - +
174J GLY* 3.8 3.4 - - - -
5N G 3.5 4.2 + - - -
6N T 2.9 33.6 + - - +
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Residues in contact with PRO 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J VAL 5.0 2.2 - - - +
32J ALA* 3.6 36.8 - - + +
33J ARG* 3.8 11.0 - - - +
35J LEU 4.5 7.0 - - - +
42J LEU 4.5 1.1 - - - +
43J LYS* 1.3 86.4 - - + +
45J VAL* 1.3 63.3 + - - +
47J ARG* 3.2 20.4 + - + +
48J ARG* 2.9 53.2 + - - +
79J HIS* 4.6 3.4 - - + -
338J LEU* 6.2 0.7 - - + -
7N A 5.0 2.7 - - - +
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Residues in contact with VAL 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ARG 5.4 0.4 + - - +
43J LYS* 4.5 5.1 - - + +
44J PRO* 1.3 78.3 - - - +
46J HIS* 1.3 73.5 + - + +
48J ARG* 3.6 2.2 + - - +
49J ILE* 3.2 45.1 + - + +
79J HIS* 3.4 40.3 - - + +
85J SER 4.3 0.2 - - - +
86J ILE* 4.0 15.5 - - + -
89J ALA* 4.0 17.7 - - + -
6N T 4.0 26.5 - - - +
7N A 3.9 8.9 + - - +
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Residues in contact with HIS 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J GLY 5.6 0.4 + - - -
42J LEU* 4.0 20.5 - - + +
43J LYS* 3.1 42.3 + - + +
45J VAL* 1.3 75.6 - - + +
47J ARG* 1.3 65.5 + - - +
49J ILE* 3.2 4.2 + - - +
50J LEU* 3.0 29.0 + - - +
89J ALA* 3.9 22.8 + - + +
92J ARG* 4.7 3.1 + - - -
93J MET* 3.9 27.3 - - + +
99J TYR* 3.8 18.3 + - - -
6N T 3.2 40.7 + - - -
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Residues in contact with ARG 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J ASP* 3.6 13.3 + - - +
40J ASP* 2.9 31.6 + - - -
42J LEU* 3.0 36.2 + - + +
43J LYS 3.1 4.1 + - - +
44J PRO* 3.5 29.2 - - - +
46J HIS* 1.3 78.8 - - - +
48J ARG* 1.3 59.0 + - + +
50J LEU* 3.3 3.8 + - - +
51J TYR* 2.9 31.9 + - - +
157J PRO* 3.3 29.2 - - + +
158J SER 3.6 13.0 + - - -
159J VAL* 3.4 14.9 - - - +
160J LEU* 3.7 20.4 - - + +
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Residues in contact with ARG 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ALA* 5.9 1.8 + - - +
44J PRO* 2.9 32.4 + - + +
45J VAL 3.9 4.3 - - - +
46J HIS 3.3 0.2 - - - -
47J ARG* 1.3 75.1 - - + +
49J ILE* 1.3 60.6 - - - +
51J TYR* 3.6 6.3 + - - +
52J GLY* 2.9 26.7 + - - -
74J VAL* 3.9 14.3 - - + +
78J TYR* 3.3 44.1 + - + -
79J HIS* 3.0 38.4 + - + +
80J PRO* 4.5 5.3 - - - +
81J HIS* 4.9 4.2 + - - -
147J ILE* 6.1 1.0 - - - +
150J TYR* 6.3 0.8 - - - +
156J GLU* 2.7 40.6 + - + +
157J PRO* 6.3 0.9 - - + -
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Residues in contact with ILE 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J VAL* 3.2 28.6 + - + +
46J HIS 3.2 6.0 + - - +
48J ARG* 1.3 75.1 - - - +
50J LEU* 1.3 57.7 + - - +
52J GLY* 3.2 2.6 + - - -
53J LEU* 2.9 41.2 + - + +
70J ILE* 5.0 4.2 - - + +
74J VAL* 3.9 14.1 - - + +
86J ILE* 3.5 41.5 - - + +
89J ALA* 4.0 2.7 - - + -
90J MET* 3.9 28.3 - - + +
93J MET* 3.6 28.9 - - + -
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Residues in contact with LEU 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J LEU* 4.1 15.7 - - + -
46J HIS 3.0 17.0 + - - +
47J ARG 3.9 3.8 - - - +
49J ILE* 1.3 73.8 - - - +
51J TYR* 1.3 61.9 + - - +
53J LEU* 3.4 20.2 + - + +
54J ASN* 3.2 21.5 + - - +
93J MET* 4.1 20.0 - - + -
103J LEU* 4.0 25.4 - - + +
104J VAL* 4.2 3.1 - - + -
132J THR* 4.0 24.5 - - + -
135J LEU* 3.6 30.7 - - + -
136J LEU* 3.7 9.7 - - + +
160J LEU* 4.4 10.5 - - + -
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Residues in contact with TYR 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J ARG 2.9 18.6 + - - +
48J ARG* 3.9 4.5 - - - +
50J LEU* 1.3 73.6 - - - +
52J GLY* 1.3 59.5 + - - +
54J ASN* 3.2 9.3 + - - +
55J GLU* 2.9 67.0 + - + +
78J TYR* 3.6 28.9 - + - -
136J LEU* 4.4 4.4 - - + +
139J ILE* 3.7 23.1 - - + -
140J ASN* 5.8 1.7 + - - -
146J PHE* 3.6 19.1 - + - -
155J ARG* 3.6 18.5 + - - +
156J GLU* 4.8 0.2 - - + -
157J PRO* 3.5 41.7 - - + -
160J LEU* 5.0 2.5 - - + -
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Residues in contact with GLY 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J ARG 2.9 16.2 + - - -
49J ILE 3.5 4.0 - - - -
51J TYR* 1.3 74.2 - - - +
53J LEU* 1.3 64.0 + - - +
55J GLU* 3.5 2.9 + - - +
56J GLN* 3.2 30.1 + - - +
70J ILE* 5.8 1.6 - - - -
73J ASP* 4.0 10.1 - - - -
74J VAL* 4.4 6.1 - - - -
78J TYR* 4.0 18.8 - - - -
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Residues in contact with LEU 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J ILE* 2.9 28.3 + - + +
50J LEU* 3.5 28.9 - - + +
52J GLY* 1.3 74.5 - - - +
54J ASN* 1.3 59.3 + - - +
57J GLY 3.3 2.8 + - - -
58J MET* 2.9 51.6 + - + +
70J ILE* 3.7 39.0 - - + +
90J MET* 5.4 2.0 - - + -
104J VAL* 4.4 11.9 - - + -
126J ALA* 5.5 0.4 - - + -
127J ARG* 4.4 17.7 - - - +
128J MET* 3.7 24.7 - - + -
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Residues in contact with ASN 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J LEU 3.2 11.1 + - - +
51J TYR* 3.2 10.7 + - - +
52J GLY 3.1 0.4 - - - -
53J LEU* 1.3 77.7 - - - +
55J GLU* 1.3 72.2 + - - +
57J GLY* 3.1 17.7 + - - -
59J THR* 5.1 2.9 - - - +
128J MET* 3.2 21.9 - - + +
133J LEU* 5.4 2.3 - - - +
136J LEU* 3.7 24.4 - - + +
139J ILE* 3.8 25.3 - - - +
140J ASN* 4.9 5.5 - - - +
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Residues in contact with GLU 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J TYR* 2.9 64.1 + - + +
52J GLY* 4.0 3.1 - - - +
54J ASN* 1.3 87.9 + - - +
56J GLN* 1.3 74.1 + - - +
57J GLY 3.3 1.7 + - - -
78J TYR* 3.6 13.2 - - - +
139J ILE* 5.6 0.2 - - - +
140J ASN* 5.0 9.2 + - - +
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Residues in contact with GLN 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J GLY 3.2 16.7 + - - +
54J ASN 3.3 0.2 - - - -
55J GLU* 1.3 91.6 + - - +
57J GLY* 1.3 64.3 + - - +
58J MET* 2.9 39.6 + - + +
73J ASP* 3.5 24.9 + - + +
77J LYS* 3.4 24.7 + - - +
78J TYR* 5.1 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
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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