Contacts of the helix formed by residues 83 - 97 (chain A) in PDB entry 4UY3
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 PRO 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ASN 3.5 12.6 - - - +
79A LYS 3.5 18.6 - - - +
80A TYR 3.8 2.0 - - - -
81A LEU 3.2 11.7 - - - +
82A ALA* 1.3 91.8 - - + +
84A VAL* 1.3 63.1 + - - +
85A GLU 3.3 0.2 - - - -
86A GLU* 3.3 11.1 + - + +
87A LYS* 3.2 24.6 + - + +
113A LEU* 4.1 14.4 - - + -
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Residues in contact with VAL 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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38A LYS* 4.4 13.2 - - + -
80A TYR 3.4 23.1 - - - +
81A LEU* 3.4 15.0 - - + +
82A ALA 3.1 1.0 + - - -
83A PRO* 1.3 74.0 - - - +
85A GLU* 1.3 67.9 + - - +
87A LYS* 3.0 19.6 + - - +
88A ILE* 3.0 34.0 + - + +
110A ALA* 4.2 7.4 - - + +
113A LEU* 4.1 12.8 - - + -
114A MET* 4.1 35.9 - - + -
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Residues in contact with GLU 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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38A LYS* 3.7 29.1 + - - +
81A LEU 4.3 1.2 + - - +
82A ALA 3.5 10.8 + - - +
83A PRO 3.3 0.2 - - - -
84A VAL* 1.3 81.2 - - - +
86A GLU* 1.3 58.2 + - - +
88A ILE* 3.3 8.8 + - - +
89A HIS* 3.0 25.5 + - + +
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Residues in contact with GLU 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 ALA 4.6 0.8 + - - +
83A PRO* 3.3 11.6 + - + +
84A VAL 3.1 1.0 - - - -
85A GLU* 1.3 76.5 - - - +
87A LYS* 1.3 67.2 + - - +
89A HIS* 2.9 11.7 + - + +
90A ASN* 2.8 45.2 + - - +
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Residues in contact with LYS 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 PRO* 3.2 14.0 + - + +
84A VAL 3.0 7.7 + - - +
86A GLU* 1.3 76.5 - - + +
88A ILE* 1.3 58.6 + - - +
90A ASN* 3.4 2.3 + - - +
91A ALA* 3.0 27.6 + - - +
106A GLU* 3.2 52.7 + - - +
107A ILE* 5.3 0.2 - - - -
109A ASP* 2.9 37.4 + - + -
110A ALA* 4.1 10.3 - - + +
113A LEU* 4.4 19.1 - - + -
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Residues in contact with ILE 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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31A ILE* 4.0 15.3 - - + -
34A ALA* 4.4 20.6 - - + +
35A ILE* 3.9 35.9 - - + -
38A LYS* 4.7 7.2 - - + -
84A VAL* 3.0 37.8 + - + +
85A GLU* 3.6 10.3 - - - +
87A LYS* 1.3 73.8 - - - +
89A HIS* 1.3 65.1 + - - +
91A ALA* 3.2 8.3 + - - +
92A GLU* 3.1 26.6 + - - +
107A ILE* 4.3 13.7 - - + -
110A ALA* 4.5 5.6 - - + -
114A MET* 5.1 0.2 - - + -
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Residues in contact with HIS 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 GLU* 3.0 14.5 + - + +
86A GLU* 2.9 13.8 + - - +
88A ILE* 1.3 77.6 - - - +
90A ASN* 1.3 70.2 + - - +
92A GLU* 3.2 18.5 + - + +
93A ALA* 3.1 27.5 + - + +
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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 GLU* 2.8 47.2 + - - +
87A LYS* 3.8 2.2 - - - +
89A HIS* 1.3 78.2 + - - +
91A ALA* 1.3 60.9 + - - +
93A ALA* 3.3 5.8 + - - +
94A LEU* 2.9 42.0 + - + +
106A GLU* 3.1 31.6 + - + +
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Residues in contact with ALA 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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31A ILE* 3.8 7.0 - - + +
87A LYS 3.0 14.7 + - - +
88A ILE 3.2 9.8 + - - +
90A ASN* 1.3 77.8 - - - +
92A GLU* 1.3 55.8 + - - +
95A LEU* 3.1 18.2 + - - +
103A SER* 2.9 33.9 + - - +
106A GLU* 4.0 7.8 - - + +
107A ILE* 3.6 33.0 - - + -
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Residues in contact with GLU 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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28A ARG* 5.1 14.4 + - - +
31A ILE* 4.1 30.3 - - + +
35A ILE* 4.2 11.4 - - - +
88A ILE* 3.1 24.6 + - - +
89A HIS* 3.2 20.4 + - + +
91A ALA* 1.3 72.6 - - - +
93A ALA* 1.3 65.8 + - - +
95A LEU* 3.4 3.6 + - - +
96A ASP* 3.0 25.2 + - - +
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Residues in contact with ALA 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 HIS* 3.1 25.0 + - + +
90A ASN* 3.8 7.4 - - - +
92A GLU* 1.3 80.4 - - - +
94A LEU* 1.3 61.6 + - + +
96A ASP* 3.5 7.7 + - - +
97A LYS* 3.3 26.1 + - - +
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Residues in contact with LEU 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* 2.9 24.5 + - + +
93A ALA* 1.3 74.6 - - + +
95A LEU* 1.3 67.1 + - - +
97A LYS* 3.2 11.1 + - + -
98A PHE 3.3 0.2 + - - -
99A SER* 2.9 45.5 + - - +
102A ALA* 3.9 22.4 - - + -
103A SER* 4.0 11.2 - - - +
106A GLU* 3.9 25.8 - - + -
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Residues in contact with LEU 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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24A ARG* 3.8 28.9 - - + +
27A LYS* 3.7 29.6 - - + -
28A ARG* 4.0 18.6 - - - +
31A ILE* 4.0 19.7 - - + -
91A ALA 3.1 20.5 + - - +
92A GLU* 3.7 4.5 - - - +
94A LEU* 1.3 75.5 - - - +
96A ASP* 1.3 55.9 + - - +
98A PHE* 2.7 27.0 + - - -
99A SER 4.6 2.5 - - - +
100A PHE* 3.7 33.9 - - + -
103A SER* 3.7 14.1 - - - +
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Residues in contact with ASP 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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24A ARG* 3.3 38.7 + - - +
28A ARG* 5.2 7.8 + - - +
92A GLU 3.0 15.3 + - - +
93A ALA* 3.5 9.8 - - - +
95A LEU* 1.3 81.7 - - - +
97A LYS* 1.3 64.1 + - - +
98A PHE* 3.5 8.1 + - - -
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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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93A ALA 3.3 13.4 + - - +
94A LEU* 3.2 11.6 + - + +
96A ASP* 1.3 81.2 - - - +
98A PHE* 1.3 76.8 + - - +
99A SER* 3.3 9.1 + - - +
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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