Contacts of the helix formed by residues 80 - 94 (chain A) in PDB entry 5BXD
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 ASP 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLY 5.6 0.2 - - - +
38A GLY* 4.6 0.4 - - - -
79A ARG* 1.3 76.7 - - - +
81A GLY* 1.3 62.0 + - - +
82A GLN* 3.1 11.3 + - - +
83A MET* 3.0 35.9 + - + +
84A PHE* 3.4 21.3 + - - +
107A LEU* 4.4 18.5 - - - +
111A GLU* 3.6 31.7 + - + +
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Residues in contact with GLY 81 (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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38A GLY* 3.5 31.7 - - - -
39A HIS* 3.3 12.0 + - - -
41A TYR* 2.6 35.0 + - - -
79A ARG 3.3 4.2 + - - -
80A ASP* 1.3 72.9 + - - +
82A GLN* 1.3 56.7 + - - +
84A PHE* 3.4 6.8 + - - -
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Residues in contact with GLN 82 (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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39A HIS* 3.4 25.0 + - + +
41A TYR* 4.1 1.8 - - - -
80A ASP* 3.1 6.9 + - - +
81A GLY* 1.3 74.7 - - - +
83A MET* 1.3 74.3 + - + +
84A PHE 3.5 0.2 + - - -
85A ARG* 3.6 12.1 + - - +
86A TYR* 3.5 17.3 - - - -
104A ASP* 4.7 8.7 - - - +
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Residues in contact with MET 83 (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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80A ASP* 3.0 31.3 + - + +
82A GLN* 1.3 91.8 - - + +
84A PHE* 1.3 64.1 + - - +
85A ARG 3.1 2.7 - - - -
86A TYR* 3.2 24.5 + - + -
87A ILE* 3.4 4.2 + - - +
102A PHE* 3.9 6.3 - - + -
104A ASP* 3.4 52.5 - - + +
107A LEU* 4.0 8.1 - - + -
108A LEU* 3.2 43.5 - - + +
111A GLU* 3.9 17.5 - - + -
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Residues in contact with PHE 84 (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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35A ASP* 3.9 22.7 - - + -
37A GLY 5.2 6.3 - - - +
41A TYR* 3.6 30.7 - + + -
48A LEU* 4.8 11.4 - - + -
56A ILE* 4.1 17.9 - - + -
77A ILE* 4.5 6.7 - - + -
79A ARG* 6.1 1.3 - - + -
80A ASP 3.4 18.4 + - - +
81A GLY* 3.6 9.6 - - - +
82A GLN 3.3 1.0 - - - -
83A MET* 1.3 77.4 - - - +
85A ARG* 1.3 58.5 + - - +
87A ILE* 3.2 14.4 + - + +
88A LEU* 2.8 50.2 + - + +
91A LEU* 5.9 0.4 - - + -
111A GLU* 6.0 0.4 - - - -
115A PHE* 3.7 37.7 - + - -
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Residues in contact with ARG 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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41A TYR* 3.2 37.9 + - + +
82A GLN 3.6 9.8 + - - +
83A MET 3.1 0.2 - - - -
84A PHE* 1.3 77.1 - - - +
86A TYR* 1.3 82.6 + - + +
88A LEU* 3.5 2.8 + - - +
89A ASN* 2.9 29.9 + - + +
92A ARG* 5.6 1.5 + - - +
80B ASP* 2.7 42.4 + - - +
82B GLN* 3.3 35.4 + - - +
83B MET* 3.3 25.1 - - - +
104B ASP* 3.1 20.6 + - - -
107B LEU* 3.6 15.0 - - - +
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Residues in contact with TYR 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 GLN 3.5 21.3 - - - -
83A MET* 3.2 19.4 + - + +
84A PHE 3.2 0.6 - - - -
85A ARG* 1.3 96.2 + - + +
87A ILE* 1.3 64.7 + - - +
89A ASN* 3.9 5.6 - - + +
90A PHE* 3.2 16.1 + - - +
95A LYS 5.3 0.3 - - - +
96A LEU* 5.5 1.5 - - + +
97A LEU 3.6 22.6 + - - +
98A ILE* 4.7 2.2 - - + -
99A PRO* 3.4 38.5 - - + +
102A PHE* 4.0 17.6 - + - -
108A LEU* 3.8 27.4 - - + -
120A MET* 3.6 13.6 - - + +
107B LEU* 4.1 18.8 - - + -
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Residues in contact with ILE 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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56A ILE* 5.3 3.4 - - + -
83A MET 3.4 13.9 + - - +
84A PHE* 3.2 22.4 + - + +
86A TYR* 1.3 77.3 - - - +
88A LEU* 1.3 63.3 + - - +
90A PHE* 3.1 14.4 + - - +
91A LEU* 3.3 19.2 + - + +
108A LEU* 4.0 7.0 - - + -
111A GLU* 4.1 5.6 - - + -
112A ALA* 3.7 31.2 - - + +
115A PHE* 3.8 28.5 - - + -
117A LEU* 4.4 14.2 - - + +
120A MET* 3.6 27.1 - - + -
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Residues in contact with LEU 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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41A TYR* 4.0 32.1 - - + -
43A SER* 3.8 25.1 - - - +
47A THR* 4.3 5.4 - - + -
48A LEU* 3.9 22.2 - - + -
84A PHE* 2.8 29.7 + - + +
85A ARG* 3.8 4.3 - - - +
87A ILE* 1.3 74.4 - - - +
89A ASN* 1.3 62.7 + - - +
91A LEU* 3.1 16.8 + - + +
92A ARG* 3.1 55.5 + - - +
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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 ARG* 2.9 19.7 + - + +
86A TYR* 4.1 7.4 - - - +
87A ILE 3.3 0.4 - - - -
88A LEU* 1.3 74.4 - - - +
90A PHE* 1.3 59.7 + - - +
92A ARG* 3.3 14.7 + - - +
93A THR* 2.9 46.2 + - - +
95A LYS 4.6 1.3 + - - -
97A LEU* 3.6 32.0 + - - +
79B ARG* 5.4 0.3 + - - -
80B ASP* 3.7 29.3 + - + +
107B LEU* 4.1 22.5 + - + +
111B GLU* 4.2 5.3 + - - +
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Residues in contact with PHE 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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50A LYS* 4.8 0.2 + - - -
51A TYR* 3.9 27.0 + + - -
86A TYR 3.2 13.5 + - - +
87A ILE 3.1 10.6 + - - +
89A ASN* 1.3 74.3 - - - +
91A LEU* 1.3 59.7 + - - +
94A SER* 2.7 41.4 + - - -
95A LYS* 3.2 43.9 + - - +
96A LEU* 3.9 4.3 - - - -
117A LEU* 3.5 22.0 - - + -
119A PRO* 3.5 18.8 - - + -
120A MET* 3.2 53.2 - - + -
123A GLU* 4.6 7.6 - - + -
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Residues in contact with LEU 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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47A THR* 3.7 32.8 - - + +
48A LEU* 4.3 16.8 - - + +
50A LYS* 3.0 34.0 + - + +
51A TYR* 3.7 29.4 - - + +
56A ILE* 4.5 17.5 - - + -
84A PHE* 5.9 1.1 - - + -
87A ILE* 3.6 15.5 - - + +
88A LEU* 3.1 26.0 + - + +
90A PHE* 1.3 77.5 - - - +
92A ARG* 1.3 57.5 + - - +
117A LEU* 3.8 23.1 - - + -
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Residues in contact with ARG 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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41A TYR* 5.7 1.8 - - - -
42A THR 3.1 21.6 + - - -
47A THR* 4.1 14.8 - - + +
50A LYS* 4.4 4.6 + - - -
85A ARG* 5.6 1.2 + - - +
88A LEU* 3.1 43.4 + - - +
89A ASN* 3.6 16.6 + - - +
91A LEU* 1.3 80.6 - - - +
93A THR* 1.3 67.3 + - + +
37B GLY* 3.2 16.2 + - - -
78B ASP* 2.8 44.0 + - - +
79B ARG* 3.2 45.4 + - - +
80B ASP* 3.3 13.3 + - - +
81B GLY 4.6 0.2 - - - +
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Residues in contact with THR 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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50A LYS* 5.0 0.4 - - - -
89A ASN* 2.9 37.4 + - - +
92A ARG* 1.3 80.0 - - + +
94A SER* 1.3 68.8 + - - +
95A LYS* 3.1 36.6 + - - +
97A LEU* 3.8 5.7 - - + +
79B ARG* 3.6 30.5 - - - +
110B GLU* 3.9 23.3 - - + +
111B GLU* 4.0 2.0 - - - +
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Residues in contact with SER 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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50A LYS* 2.8 27.8 + - - +
51A TYR* 3.4 17.2 + - - -
90A PHE* 2.7 33.2 + - - -
92A ARG 3.6 1.2 - - - -
93A THR* 1.3 73.3 - - - +
95A LYS* 1.3 60.5 + - - +
123A GLU* 5.6 2.4 - - - +
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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