Contacts of the helix formed by residues 81 - 98 (chain A) in PDB entry 4U86
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A HIS* 3.7 0.7 - - - -
65A SER* 4.4 7.4 - - - +
79A THR 4.8 3.4 - - - +
80A ARG* 1.4 76.5 - - - +
82A LYS* 1.3 59.3 + - - +
83A GLU* 3.5 18.9 + - - +
84A GLU* 3.0 38.1 + - - +
85A ALA* 2.9 27.9 + - - +
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Residues in contact with LYS 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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64A HIS* 3.7 43.1 + - + +
65A SER* 5.1 1.0 + - - +
66A GLN* 4.9 16.1 + - + +
81A THR* 1.3 71.7 - - - +
83A GLU* 1.3 70.1 + - + +
85A ALA* 3.1 3.3 + - - +
86A LEU* 2.9 28.8 + - + +
151A PHE* 4.3 21.3 - - + -
156A ILE* 3.8 9.4 - - + +
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Residues in contact with GLU 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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81A THR* 3.2 19.8 - - - +
82A LYS* 1.3 89.2 + - + +
84A GLU* 1.3 55.7 + - + +
86A LEU* 3.3 9.1 + - - +
87A GLU* 3.0 32.7 + - - +
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Residues in contact with GLU 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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80A ARG* 3.3 18.1 - - + +
81A THR* 3.0 44.9 + - - +
83A GLU* 1.3 71.3 - - + +
85A ALA* 1.3 65.8 + - - +
87A GLU* 3.2 9.2 + - - +
88A LEU* 3.0 31.2 + - + +
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Residues in contact with ALA 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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62A VAL* 3.7 20.8 - - + +
63A LYS 4.0 6.3 - - - +
64A HIS* 4.0 10.3 - - + -
80A ARG* 3.8 15.1 - - - +
81A THR 2.9 13.9 + - - +
82A LYS 3.1 8.9 + - - +
84A GLU* 1.3 77.4 - - - +
86A LEU* 1.3 57.0 + - - +
88A LEU* 3.3 4.6 + - - +
89A ILE* 2.9 31.9 + - - +
156A ILE* 3.7 14.4 - - + -
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Residues in contact with LEU 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 LYS* 2.9 16.9 + - + +
83A GLU* 3.7 8.5 - - - +
85A ALA* 1.3 79.1 - - - +
87A GLU* 1.3 56.9 + - + +
89A ILE* 3.3 2.0 + - + -
90A ASN* 2.8 44.0 + - - +
149A PRO* 3.7 37.2 - - + -
151A PHE* 4.0 20.9 - - + -
156A ILE* 3.5 12.3 - - + +
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Residues in contact with GLU 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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83A GLU 3.0 19.5 + - - +
84A GLU* 3.2 11.0 + - - +
86A LEU* 1.3 76.3 - - + +
88A LEU* 1.3 64.1 + - + +
90A ASN* 3.4 11.1 + - - +
91A GLY* 3.0 20.3 + - - -
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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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62A VAL* 4.1 9.0 - - + -
80A ARG* 3.5 37.9 - - - +
84A GLU* 3.0 20.5 + - + +
85A ALA 3.5 6.3 - - - +
86A LEU 3.2 0.2 - - - -
87A GLU* 1.3 78.1 - - + +
89A ILE* 1.3 62.5 + - - +
91A GLY* 3.2 3.2 + - - -
92A TYR* 3.0 56.8 + - + +
95A LYS* 5.1 0.2 + - - -
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Residues in contact with ILE 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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60A LEU* 4.2 6.7 - - + +
62A VAL* 3.7 19.7 - - + -
85A ALA 2.9 17.6 + - - +
86A LEU* 3.6 8.1 - - - +
88A LEU* 1.3 76.2 - - - +
90A ASN* 1.3 64.3 + - - +
92A TYR* 3.2 6.8 + - - +
93A ILE* 2.9 26.1 + - + +
149A PRO* 3.7 35.4 - - + -
156A ILE* 3.5 38.8 - - + +
157A HIS 4.2 0.2 - - - -
158A ILE* 3.8 31.1 - - + +
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Residues in contact with ASN 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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86A LEU* 2.8 38.0 + - - +
87A GLU* 3.8 12.2 + - - +
88A LEU 3.2 0.2 - - - -
89A ILE* 1.3 77.8 - - - +
91A GLY* 1.3 55.9 + - - +
93A ILE* 3.4 8.5 + - - +
94A GLN* 3.0 35.9 + - + +
149A PRO* 3.4 26.7 - - - +
300A 1PG 6.1 0.9 - - - +
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Residues in contact with GLY 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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87A GLU 3.0 14.7 + - - -
88A LEU* 3.2 3.8 + - - -
90A ASN* 1.3 71.2 - - - +
92A TYR* 1.3 65.6 + - - +
94A GLN* 3.3 15.8 + - - +
95A LYS* 3.0 41.0 + - - +
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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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60A LEU* 3.9 21.1 - - + -
62A VAL* 3.9 21.4 - - + +
74A ARG* 4.9 3.8 + - - -
88A LEU* 3.0 46.4 + - + +
89A ILE* 3.2 9.4 + - - +
91A GLY* 1.3 76.0 - - - +
93A ILE* 1.3 62.4 + - - +
95A LYS* 3.2 19.7 + - - +
96A ILE* 3.0 29.7 + - + +
106A LEU* 4.0 24.2 - - + -
110A PHE* 3.3 51.1 - + + +
158A ILE* 3.9 10.5 - - + -
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Residues in contact with ILE 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 ILE* 2.9 28.5 + - + +
90A ASN* 3.7 11.7 - - - +
92A TYR* 1.3 74.1 - - - +
94A GLN* 1.3 60.0 + - + +
96A ILE* 3.3 7.0 + - - +
97A LYS* 2.9 33.5 + - + +
146A MET* 4.1 13.7 - - + -
147A SER 4.4 1.1 - - - +
148A GLY* 4.1 9.6 - - - -
149A PRO* 3.7 33.9 - - + -
158A ILE* 3.7 22.0 - - + -
300A 1PG 3.5 36.8 - - - +
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Residues in contact with GLN 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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90A ASN* 3.0 19.2 + - + +
91A GLY* 3.6 15.1 + - - +
92A TYR 3.3 0.2 - - - -
93A ILE* 1.3 79.0 - - + +
95A LYS* 1.3 57.4 + - + +
97A LYS* 3.3 4.7 + - - +
98A SER* 2.9 32.1 + - - -
100A GLU* 5.2 0.7 - - - -
300A 1PG 5.5 9.9 - - - +
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Residues in contact with LYS 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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88A LEU 5.1 0.2 + - - -
91A GLY* 3.0 38.3 + - - +
92A TYR* 3.7 25.3 - - + +
94A GLN* 1.3 74.0 - - + +
96A ILE* 1.3 64.2 + - - +
98A SER* 3.0 19.8 + - - -
100A GLU* 3.2 33.2 + - + +
101A GLU* 3.3 32.4 + - + +
106A LEU* 4.5 7.0 - - + -
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Residues in contact with ILE 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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60A LEU* 5.3 1.1 - - + -
92A TYR* 3.0 22.4 + - + +
93A ILE* 3.8 4.7 - - - +
95A LYS* 1.3 74.9 - - - +
97A LYS* 1.3 63.7 + - - +
99A GLY* 3.2 13.3 + - - -
101A GLU 3.5 7.5 - - - +
102A ASP* 5.4 0.2 - - - -
103A PHE* 3.9 52.5 - - + +
106A LEU* 3.6 21.3 - - + -
146A MET* 3.9 26.9 - - + -
158A ILE* 4.6 9.6 - - + -
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Residues in contact with LYS 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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32A SER 3.2 12.7 + - - -
93A ILE* 2.9 21.8 + - + +
94A GLN* 3.8 4.9 - - - +
96A ILE* 1.3 77.6 - - - +
98A SER* 1.3 59.8 + - - +
99A GLY 3.5 0.5 + - - -
146A MET* 4.3 15.3 - - + -
300A 1PG 2.9 90.2 - - - +
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Residues in contact with SER 98 (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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94A GLN 2.9 15.4 + - - -
95A LYS 3.0 16.3 + - - -
96A ILE 3.2 0.2 - - - -
97A LYS* 1.3 76.1 - - - +
99A GLY* 1.3 58.3 + - - +
100A GLU* 2.7 37.9 + - - +
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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