Contacts of the helix formed by residues 56 - 68 (chain B) in PDB entry 2R2Q
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 THR 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASP 4.6 4.9 - - - +
55B LEU* 1.3 76.8 - - - +
57B VAL* 1.3 66.3 + - - +
58B GLY* 3.5 2.4 + - - -
59B GLN* 2.9 47.6 + - + +
60B PHE* 3.0 21.1 + - - +
87B THR 3.5 12.7 + - - +
88B SER* 4.3 16.2 - - - +
89B ALA 3.3 8.1 - - - +
90B THR* 4.1 5.2 - - + +
91B MET* 4.0 1.1 - - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MPD 3.4 20.4 - - + -
56B THR* 1.3 72.3 - - - +
58B GLY* 1.3 58.0 + - - +
60B PHE* 3.2 1.7 + - - +
61B TYR* 2.8 28.4 + - - +
78B PHE* 4.3 10.8 - - + -
85B PRO* 4.1 7.6 - - + -
86B PRO 3.4 19.5 - - - +
87B THR 3.5 0.2 + - - -
89B ALA* 2.8 25.6 + - + +
90B THR 4.0 2.9 - - - +
91B MET* 3.9 15.7 - - - -
94B LEU* 3.8 46.2 - - + -
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MPD 4.5 2.5 - - - -
56B THR* 3.2 1.1 - - - -
57B VAL* 1.3 75.6 - - - +
59B GLN* 1.3 61.3 + - - +
61B TYR* 3.2 10.6 + - - +
62B PHE* 3.0 35.8 + - - -
87B THR* 2.9 34.3 + - - +
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Residues in contact with GLN 59 (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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54B ASP 4.4 1.4 - - - +
55B LEU* 3.3 26.9 - - + +
56B THR* 2.9 49.6 + - - +
58B GLY* 1.3 75.5 - - - +
60B PHE* 1.3 62.5 + - - +
62B PHE* 3.3 10.4 + - + +
63B LEU* 3.1 26.0 + - - +
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Residues in contact with PHE 60 (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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31B VAL* 4.2 4.5 - - + -
33B VAL* 3.5 34.1 - - + -
49B TYR* 4.1 13.5 - + + -
51B VAL* 3.5 34.1 - - + -
55B LEU* 4.1 7.3 - - + +
56B THR 3.0 12.3 + - - +
57B VAL 3.2 6.9 + - - +
59B GLN* 1.3 73.1 - - - +
61B TYR* 1.3 67.9 + - - +
63B LEU* 3.0 19.4 + - + +
64B ILE* 2.9 42.8 + - + +
78B PHE* 3.9 17.9 - + - -
91B MET* 3.6 35.4 - - + -
107B VAL* 4.8 3.4 - - + -
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MPD 3.5 34.3 - - + +
57B VAL 2.8 13.4 + - - +
58B GLY* 3.3 14.1 - - - +
60B PHE* 1.3 75.3 - - - +
62B PHE* 1.3 80.5 + + - +
64B ILE* 3.2 3.6 + - - +
65B ARG* 2.9 63.5 + - + +
76B LEU* 2.6 48.3 + - + -
77B PHE* 4.4 1.3 - - - -
78B PHE* 3.6 32.8 - + + -
87B THR* 6.5 0.2 - - + -
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Residues in contact with PHE 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 GLY* 3.0 30.5 + - - -
59B GLN* 3.3 9.8 + - + +
60B PHE 3.3 0.4 - - - -
61B TYR* 1.3 95.5 - + - +
63B LEU* 1.3 64.0 + - + +
65B ARG* 3.4 22.9 + - + +
66B LYS* 3.0 23.7 + - - +
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Residues in contact with LEU 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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55B LEU* 3.9 29.2 - - + -
59B GLN* 3.1 14.8 + - + +
60B PHE* 3.0 19.6 + - + +
62B PHE* 1.3 77.5 - - + +
64B ILE* 1.3 62.4 + - + +
66B LYS* 3.3 17.0 + - + +
67B ARG* 3.1 21.3 + - - +
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Residues in contact with ILE 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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33B VAL* 4.2 15.3 - - + -
44B LEU* 4.3 10.3 - - + -
49B TYR* 3.9 35.9 - - + +
60B PHE* 2.9 38.3 + - + +
61B TYR 3.7 6.7 - - - +
63B LEU* 1.3 74.9 - - + +
65B ARG* 1.3 66.1 + - - +
67B ARG* 3.1 14.8 + - - +
68B ILE* 3.1 31.9 + - + +
76B LEU* 4.5 3.4 - - + -
78B PHE* 3.9 28.5 - - + -
109B TYR* 4.4 3.1 - - + -
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Residues in contact with ARG 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 TYR* 2.9 55.9 + - + +
62B PHE* 3.4 26.3 + - + +
64B ILE* 1.3 76.5 - - - +
66B LYS* 1.3 62.1 + - - +
68B ILE* 3.3 3.6 + - - +
69B HIS 3.1 17.2 + - - -
70B LEU* 3.3 30.1 + - + +
71B ARG 2.9 28.3 + - - -
72B PRO* 3.3 16.4 + - - +
74B ASP 2.9 27.7 + - - -
76B LEU* 3.7 32.4 - - + +
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Residues in contact with LYS 66 (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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62B PHE 3.0 13.5 + - - +
63B LEU* 3.4 19.7 - - + +
64B ILE 3.1 0.2 - - - -
65B ARG* 1.3 77.1 - - - +
67B ARG* 1.3 60.9 + - - +
69B HIS* 3.1 25.8 + - - +
70B LEU 5.3 0.7 - - - +
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Residues in contact with ARG 67 (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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1A UNX 3.9 17.6 - - - -
81A ASN* 5.9 1.0 - - - +
98A ASN 5.2 1.6 + - - -
99A HIS* 2.9 29.5 + - - -
100A GLU* 3.5 15.8 - - - +
101A GLU* 2.9 33.5 + - + +
44B LEU* 3.7 19.9 - - + +
46B LYS* 3.4 26.9 - - - +
49B TYR* 3.3 28.9 + - - -
63B LEU 3.1 12.2 + - - +
64B ILE* 3.1 13.2 + - - +
66B LYS* 1.3 76.1 - - - +
68B ILE* 1.3 56.6 + - - +
69B HIS* 3.5 18.0 + - - -
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Residues in contact with ILE 68 (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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41B VAL* 4.8 1.1 - - + -
42B PRO* 3.4 48.1 - - + +
44B LEU* 3.8 24.0 - - + -
64B ILE* 3.1 30.9 + - + +
65B ARG 3.8 3.8 - - - +
66B LYS 3.2 0.2 - - - -
67B ARG* 1.3 75.1 - - - +
69B HIS* 1.3 70.7 + - - +
70B LEU* 3.5 15.6 + - + +
76B LEU* 4.1 14.8 - - + -
109B TYR* 3.6 34.8 - - + +
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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