Contacts of the helix formed by residues 84 - 97 (chain A) in PDB entry 2B33
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 TYR 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.8 26.5 - - + -
79A THR* 4.5 5.4 - - + -
80A THR* 3.9 15.3 + - - -
81A SER* 3.3 35.4 - - - +
82A MET 3.0 0.6 - - - -
83A ASP* 1.3 76.8 - - + +
85A PHE* 1.3 56.5 + - - +
86A GLN 3.5 2.2 + - - -
87A ARG* 3.4 23.9 + - - +
88A VAL* 2.9 46.8 + - + +
105A PHE* 4.8 0.4 - - - -
116A GLU* 4.0 34.0 + - + +
44B GLN* 5.7 1.6 - - - +
50B LYS* 3.2 23.2 + - - -
84B TYR* 4.0 2.9 - - - -
116B GLU* 3.3 28.3 + - - -
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Residues in contact with PHE 85 (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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81A SER 4.7 0.2 + - - -
82A MET* 2.9 25.9 + - + +
83A ASP 3.3 1.0 - - - -
84A TYR* 1.3 75.9 - - - +
86A GLN* 1.3 84.3 + - - +
88A VAL* 3.8 0.5 - - - +
89A ASN* 2.9 61.6 + - - +
103A ARG* 4.1 9.4 - - - -
105A PHE* 3.8 50.3 - + + -
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Residues in contact with GLN 86 (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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82A MET 4.7 2.3 - - - +
83A ASP 4.7 6.1 + - - +
84A TYR 3.5 0.6 - - - -
85A PHE* 1.3 103.1 + - + +
87A ARG* 1.3 61.4 - - + +
89A ASN* 3.4 6.3 + - - +
90A GLU* 3.1 26.1 + - - +
83B ASP* 6.0 2.0 - - - +
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Residues in contact with ARG 87 (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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46A THR* 6.0 0.8 - - - -
47A ILE* 3.8 30.2 - - + +
48A GLU* 3.4 31.3 + - - +
83A ASP 3.6 15.4 + - - -
84A TYR* 3.4 23.1 + - - +
85A PHE 3.4 0.2 - - - -
86A GLN* 1.3 76.7 - - + +
88A VAL* 1.3 64.2 + - - +
90A GLU* 3.4 26.4 - - - +
91A VAL* 3.4 15.8 + - - +
80B THR* 5.0 4.4 + - - -
81B SER* 4.5 19.8 - - - -
83B ASP* 4.6 18.4 + - - +
84B TYR* 2.8 31.2 + - - -
116B GLU* 3.4 12.9 + - - -
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Residues in contact with VAL 88 (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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47A ILE* 4.0 9.6 - - + -
51A THR* 3.6 32.9 - - + +
77A VAL* 4.5 5.6 - - + -
79A THR* 4.9 0.2 - - + -
84A TYR* 2.9 40.7 + - + +
85A PHE 3.8 2.7 - - - +
87A ARG* 1.3 73.3 - - - +
89A ASN* 1.3 59.6 + - - +
91A VAL* 3.3 4.2 + - - +
92A TYR* 2.8 34.8 + - + +
105A PHE* 3.6 28.3 - - + -
117A ILE* 4.2 20.9 - - + -
119A ILE* 5.1 2.5 - - + -
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Residues in contact with ASN 89 (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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85A PHE* 2.9 53.7 + - - +
86A GLN* 3.6 6.9 - - - +
88A VAL* 1.3 75.7 - - - +
90A GLU* 1.3 51.0 + - - +
92A TYR* 3.6 7.2 - - - +
93A SER* 2.7 43.8 + - - +
103A ARG* 3.2 30.8 + - - +
105A PHE* 3.6 13.2 - - - -
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Residues in contact with GLU 90 (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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48A GLU* 4.1 14.8 - - - +
86A GLN 3.1 12.2 + - - +
87A ARG* 3.4 23.6 - - - +
89A ASN* 1.3 77.9 - - - +
91A VAL* 1.3 62.5 + - + +
93A SER* 3.7 13.0 + - - -
94A ARG* 3.6 41.9 + - - +
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Residues in contact with VAL 91 (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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48A GLU* 3.5 41.5 - - + +
51A THR* 3.9 19.5 - - + -
52A GLU* 3.9 19.5 - - + +
55A LEU* 4.2 4.9 - - + -
87A ARG 3.4 8.3 + - - +
88A VAL 3.3 6.1 + - - +
90A GLU* 1.3 74.4 - - + +
92A TYR* 1.3 66.8 + - - +
94A ARG* 3.1 28.6 + - - +
95A TYR* 3.4 13.4 - - + -
130A EDO 3.9 21.3 - - - +
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Residues in contact with TYR 92 (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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55A LEU* 3.8 23.5 - - + +
75A VAL* 3.3 44.5 - - + +
77A VAL* 4.4 11.2 - - + -
88A VAL* 2.8 22.3 + - + +
89A ASN* 3.6 9.4 - - - +
91A VAL* 1.3 76.7 - - - +
93A SER* 1.3 59.4 + - - +
95A TYR* 3.0 8.5 + - - +
96A PHE* 2.9 58.4 + + + -
101A PRO* 3.8 12.0 + - + +
103A ARG* 3.5 38.9 - - - +
119A ILE* 4.7 4.7 - - + -
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Residues in contact with SER 93 (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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89A ASN* 2.7 29.2 + - - +
90A GLU* 3.7 9.0 - - - -
91A VAL 3.3 0.2 - - - -
92A TYR* 1.3 74.8 - - - +
94A ARG* 1.3 59.7 + - - +
95A TYR 3.2 0.2 - - - -
96A PHE 4.6 0.7 - - - -
97A GLY* 2.8 36.8 + - - +
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Residues in contact with ARG 94 (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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48A GLU* 5.6 2.2 - - - +
90A GLU* 3.6 49.0 + - - +
91A VAL* 3.1 19.2 + - - +
93A SER* 1.3 77.5 - - - +
95A TYR* 1.3 65.6 + - + +
130A EDO 3.3 35.3 + - - -
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Residues in contact with TYR 95 (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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52A GLU* 3.8 4.6 + - - +
55A LEU* 3.7 45.3 - - + -
56A GLU* 2.8 37.9 + - - +
59A LYS* 4.2 11.2 - - + -
69A LEU* 3.8 34.3 - - + +
91A VAL* 3.4 21.8 - - + -
92A TYR 3.0 6.9 + - - +
94A ARG* 1.3 84.1 - - + +
96A PHE* 1.3 75.4 + - + +
97A GLY 3.8 1.1 - - - -
99A HIS* 3.5 19.9 + - - -
130A EDO 3.5 31.5 + - - -
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Residues in contact with PHE 96 (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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55A LEU* 3.8 24.7 - - + -
58A LEU* 3.9 17.5 - - + -
69A LEU* 3.6 49.1 - - + -
72A VAL* 3.8 19.7 - - + -
75A VAL* 4.5 2.9 - - + -
92A TYR* 2.9 49.4 + + + +
93A SER* 4.5 1.6 - - - -
95A TYR* 1.3 83.3 - - + +
97A GLY* 1.3 57.6 + - - +
98A ASP 3.3 2.7 - - - -
99A HIS* 4.0 7.4 - + - -
100A ARG* 3.0 26.1 + - - +
101A PRO* 3.7 27.1 - - + -
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Residues in contact with GLY 97 (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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93A SER* 2.8 34.2 + - - -
95A TYR 3.8 1.4 - - - -
96A PHE* 1.3 72.3 - - - +
98A ASP* 1.3 63.6 + - - +
100A ARG* 3.4 19.9 + - - +
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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