Contacts of the helix formed by residues 47 - 65 (chain B) in PDB entry 2Q9Q
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 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ALA* 4.5 14.1 - - + +
44B LEU* 6.3 1.3 - - - -
45B GLU* 3.6 29.6 + - - +
46B SER* 1.3 82.3 + - - +
48B PRO* 1.3 64.1 - - - +
49B GLU* 3.1 21.1 - - - +
50B ILE* 3.2 23.2 + - + -
51B VAL* 3.1 26.8 + - - +
92B TYR* 3.5 26.4 + - + +
96B ARG* 5.3 0.6 - - - +
216B ALA* 4.7 11.9 + - - +
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Residues in contact with PRO 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 3.2 22.4 - - - +
47B LYS* 1.3 89.6 - - - +
49B GLU* 1.3 79.1 + - + +
50B ILE 3.2 0.3 + - - -
51B VAL* 3.3 7.2 + - + +
52B GLU* 2.9 27.6 + - - +
123B SER* 5.2 10.3 - - - -
124B PRO* 5.8 3.6 - - + -
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER 4.6 0.7 - - - +
47B LYS* 3.1 33.8 - - - +
48B PRO* 1.3 93.2 - - + +
50B ILE* 1.3 71.5 + - + +
52B GLU* 4.2 3.4 - - - +
53B CYS* 3.2 34.2 + - - -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.4 13.5 - - + +
29B ARG* 3.6 42.0 - - + +
30B LEU* 4.1 35.2 - - + +
33B ALA* 5.3 2.9 - - + -
47B LYS* 3.2 31.3 + - + +
48B PRO 3.1 0.8 - - - -
49B GLU* 1.3 90.0 - - + +
51B VAL* 1.3 68.3 + - + +
52B GLU 3.3 0.2 + - - -
53B CYS* 3.3 2.6 + - - +
54B VAL* 3.0 33.1 + - + +
92B TYR* 6.1 0.9 - - + -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 5.8 0.2 - - + -
47B LYS 3.1 17.9 + - - +
48B PRO* 3.3 7.6 + - + +
50B ILE* 1.3 79.3 - - + +
52B GLU* 1.3 57.2 + - - +
54B VAL* 3.2 3.2 + - - +
55B MET* 2.9 37.3 + - + +
89B LEU* 3.9 24.5 - - + -
92B TYR* 4.2 22.7 - - + -
93B LEU* 4.5 22.9 - - + -
128C LEU* 5.2 8.5 - - + +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO 2.9 17.3 + - - +
49B GLU* 4.2 5.2 - - - +
51B VAL* 1.3 77.1 - - - +
53B CYS* 1.3 60.6 + - - +
55B MET* 3.0 13.6 + - - +
56B GLU* 2.8 64.7 + - - +
128C LEU 5.4 3.1 - - - +
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Residues in contact with CYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.5 28.0 - - + -
49B GLU* 3.2 24.1 + - - +
50B ILE 3.3 1.6 + - - -
52B GLU* 1.3 81.5 - - - +
54B VAL* 1.3 57.7 + - - +
56B GLU* 3.5 17.9 + - - +
57B GLN* 3.0 32.4 + - + +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.9 23.6 - - + +
27B ILE* 4.9 5.4 - - + -
30B LEU* 4.3 20.9 - - + -
50B ILE* 3.0 26.3 + - + +
51B VAL* 3.5 9.2 - - - +
53B CYS* 1.3 74.9 - - - +
55B MET* 1.3 66.4 + - - +
57B GLN* 3.5 4.6 + - + +
58B LEU* 3.0 31.3 + - + +
85B ILE* 3.6 29.8 - - + -
89B LEU* 4.2 18.8 - - + -
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Residues in contact with MET 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 2.9 25.5 + - + +
52B GLU* 3.0 16.1 + - - +
54B VAL* 1.3 78.3 - - - +
56B GLU* 1.3 57.1 + - + +
58B LEU* 3.4 8.7 + - - +
59B GLU* 2.8 50.3 + - - +
89B LEU* 3.6 25.4 - - + -
93B LEU* 6.3 0.2 - - - -
128C LEU* 3.3 16.8 - - + +
129C GLY* 3.0 38.8 - - - +
133C GLY* 4.3 1.1 - - - -
134C LEU* 3.8 25.1 - - + +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 2.8 49.9 + - - +
53B CYS* 3.6 18.8 - - - +
55B MET* 1.3 73.3 - - - +
57B GLN* 1.3 58.3 + - + +
59B GLU* 3.0 8.5 + - - +
60B HIS* 2.8 54.2 + - + +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 4.0 32.3 - - + +
23B PRO* 3.3 32.3 - - - +
26B LEU* 3.8 16.6 - - + +
27B ILE* 6.1 1.1 - - + -
53B CYS 3.0 19.3 + - - +
54B VAL* 3.7 7.4 - - + +
56B GLU* 1.3 79.6 - - + +
58B LEU* 1.3 58.8 + - + +
60B HIS* 3.9 10.7 - - - +
61B MET* 3.0 33.9 + - - +
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.6 9.6 - - + -
54B VAL* 3.0 30.3 + - + +
55B MET* 3.6 10.5 - - - +
57B GLN* 1.3 77.8 - - + +
59B GLU* 1.3 57.7 + - - +
62B GLU* 2.8 37.1 + - - +
82B MET* 2.9 37.9 - - + +
85B ILE* 4.0 19.7 - - + -
86B ARG* 4.3 37.5 - - + +
89B LEU* 4.7 10.5 - - + -
134C LEU* 6.3 0.7 - - + -
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B MET* 2.8 53.6 + - - +
56B GLU* 3.4 10.3 - - - +
58B LEU* 1.3 83.3 - - - +
60B HIS* 1.3 65.1 + - + +
62B GLU* 3.2 15.1 + - - +
63B GLU* 3.0 23.4 + - - +
129C GLY* 4.6 1.7 - - - -
130C GLY* 4.5 13.1 + - - +
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 2.8 46.0 + - + +
57B GLN* 3.9 12.6 - - - +
59B GLU* 1.3 73.5 - - + +
61B MET* 1.3 63.0 + - - +
63B GLU* 3.0 9.2 + - - +
64B ASN* 2.9 31.3 + - - +
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Residues in contact with MET 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TYR 4.3 5.4 - - - +
29A ILE* 4.4 21.5 - - + -
57B GLN* 3.0 17.4 + - - +
60B HIS* 1.3 76.6 - - - +
62B GLU* 1.3 62.9 + - - +
63B GLU 3.3 0.3 + - - -
64B ASN* 3.3 30.0 + - - +
65B LEU* 3.2 20.3 + - + +
78B HIS* 3.3 47.6 - - + +
81B GLU* 5.9 0.2 - - - +
82B MET* 3.3 35.0 - - + -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 2.8 24.1 + - - +
59B GLU* 3.4 15.9 - - - +
61B MET* 1.3 72.4 - - - +
63B GLU* 1.3 61.2 + - - +
65B LEU* 3.1 31.2 - - + +
82B MET* 3.3 10.8 - - + +
86B ARG* 4.9 11.8 + - - -
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU 3.0 12.1 + - - +
60B HIS* 3.0 9.2 + - - +
62B GLU* 1.3 73.8 - - - +
64B ASN* 1.3 55.9 + - - +
65B LEU 2.7 25.8 + - - +
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Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS* 2.9 35.8 + - - +
61B MET* 3.3 27.8 + - - +
63B GLU* 1.3 75.5 - - - +
65B LEU* 1.3 61.2 + - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET* 3.2 16.4 - - - +
62B GLU* 3.1 32.1 - - + +
63B GLU 2.7 12.9 + - - +
64B ASN* 1.3 81.1 - - + +
75B VAL* 4.3 22.7 - - + -
78B HIS* 4.7 15.0 - - + -
79B GLN* 3.1 43.3 - - + +
82B MET* 4.4 7.6 - - - -
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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