Contacts of the helix formed by residues 88 - 103 (chain A) in PDB entry 3URZ
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 ASN 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.1 37.0 + - + +
86A ASN* 3.3 7.3 - - + +
87A ARG* 1.3 74.5 - - - +
89A TYR* 1.3 61.1 + - - +
90A ASP* 3.7 10.4 + - - +
91A LYS* 3.3 37.6 + - - +
92A ALA* 3.2 18.0 + - - +
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Residues in contact with TYR 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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84A LYS* 4.3 18.6 + - + -
87A ARG* 3.3 37.4 + - + +
88A ASN* 1.3 71.4 - - - +
90A ASP* 1.3 64.1 + - - +
92A ALA* 3.9 5.0 - - - +
93A TYR* 3.2 23.2 + - - +
116A MSE 3.9 27.2 - - + +
119A CYS* 3.4 46.5 - - + -
120A ARG* 3.5 25.2 - - + +
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 3.3 8.8 - - - +
89A TYR* 1.3 78.0 - - - +
91A LYS* 1.3 63.8 + - + +
93A TYR* 3.5 5.2 + - - +
94A LEU* 3.2 19.8 + - - +
120A ARG* 3.1 37.5 + - - +
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Residues in contact with LYS 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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58A GLU* 2.8 41.3 + - - +
83A TYR* 3.4 32.8 - - + -
88A ASN* 3.3 25.7 + - - +
90A ASP* 1.3 77.3 - - + +
92A ALA* 1.3 63.9 + - - +
94A LEU* 3.2 30.0 + - + +
95A PHE* 3.2 19.9 + - + -
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Residues in contact with ALA 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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80A ALA* 4.0 12.2 - - - +
83A TYR* 3.7 7.0 - - - +
84A LYS* 3.9 18.2 - - + +
88A ASN 3.2 16.8 + - - +
89A TYR* 3.9 3.4 - - - +
90A ASP 3.4 0.2 - - - -
91A LYS* 1.3 77.0 - - - +
93A TYR* 1.3 58.4 + - - +
95A PHE* 3.6 1.4 + - - -
96A TYR* 3.1 36.5 + - + -
116A MSE 3.5 29.4 - - + -
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Residues in contact with TYR 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 TYR 3.2 16.4 + - - +
90A ASP 3.7 5.8 - - - +
91A LYS 3.3 0.2 - - - -
92A ALA* 1.3 77.1 - - - +
94A LEU* 1.3 59.1 + - + +
96A TYR* 3.3 2.4 + - - -
97A LYS* 2.8 72.0 + - + +
113A CYS* 4.0 27.6 - - + -
116A MSE 4.1 11.4 - - + +
117A GLN* 3.2 40.9 + - + -
120A ARG* 3.4 27.8 - - - -
125A ASP* 4.2 3.5 + - - -
128A ARG* 5.6 1.7 + - - -
129A MSE 4.8 6.4 - - - -
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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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58A GLU* 4.3 14.4 - - - +
62A TRP* 4.1 28.2 - - + +
90A ASP 3.2 10.8 + - - +
91A LYS* 3.2 26.6 + - + +
93A TYR* 1.3 82.3 - - + +
95A PHE* 1.3 60.8 + - + +
97A LYS* 3.5 13.2 + - + +
98A GLU* 3.0 25.5 + - - +
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Residues in contact with PHE 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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58A GLU* 3.5 42.2 - - + -
61A TYR* 3.7 25.1 - + - -
62A TRP* 3.5 30.7 - + - -
76A ALA* 3.8 26.9 - - + +
79A LEU* 3.9 24.0 - - + -
80A ALA* 3.9 14.6 - - + +
83A TYR* 4.0 14.8 - + - -
91A LYS* 3.2 22.0 + - + +
94A LEU* 1.3 79.3 - - + +
96A TYR* 1.3 63.6 + - - +
97A LYS 3.2 1.1 - - - -
98A GLU* 3.2 7.8 + - + +
99A LEU* 3.1 26.3 + - - +
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Residues in contact with TYR 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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77A THR* 5.3 6.3 - - + -
80A ALA* 3.6 31.9 - - + -
81A LEU* 3.4 30.0 + - + +
84A LYS* 3.5 19.5 - - + -
92A ALA 3.1 24.3 + - - +
93A TYR* 4.0 2.2 - - - +
95A PHE* 1.3 75.8 - - - +
97A LYS* 1.3 56.5 + - - +
99A LEU* 3.4 20.5 + - + +
100A LEU* 2.9 22.3 + - - +
109A CSX 4.8 3.5 - - - +
112A ALA* 3.3 31.2 - - + -
113A CYS* 3.4 29.0 - - - +
116A MSE 3.9 23.8 - - + -
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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 TYR* 2.8 53.1 + - + +
94A LEU* 3.6 13.5 - - + +
96A TYR* 1.3 76.3 - - - +
98A GLU* 1.3 61.7 + - - +
100A LEU* 3.3 8.9 + - + +
101A GLN* 3.2 41.0 + - + +
113A CYS* 3.7 9.1 - - - -
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Residues in contact with GLU 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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61A TYR* 4.5 16.2 - - - +
62A TRP* 4.5 17.9 - - + -
76A ALA* 5.2 2.0 - - + -
94A LEU 3.0 14.3 + - - +
95A PHE* 3.2 16.5 + - + +
97A LYS* 1.3 75.8 - - - +
99A LEU* 1.3 61.6 + - - +
101A GLN* 3.8 22.2 + - - +
102A LYS* 3.6 19.5 + - - +
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Residues in contact with LEU 99 (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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73A SER* 3.5 39.5 - - - +
76A ALA* 3.7 15.9 - - + +
77A THR* 3.5 28.3 - - + +
95A PHE 3.1 15.0 + - - +
96A TYR* 3.5 34.3 - - + +
98A GLU* 1.3 73.6 - - - +
100A LEU* 1.3 65.7 + - - +
101A GLN 3.3 0.4 - - - -
102A LYS* 3.2 23.3 + - + +
103A ALA* 3.7 5.5 + - - +
109A CSX 4.0 23.7 + - + +
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Residues in contact with LEU 100 (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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96A TYR 2.9 16.2 + - - +
97A LYS* 3.3 12.7 + - + +
99A LEU* 1.3 78.4 - - - +
101A GLN* 1.3 55.9 + - - +
103A ALA 4.0 3.1 - - - +
104A PRO* 3.1 43.5 - - + +
109A CSX 3.6 26.6 - - + +
110A LEU* 3.5 28.0 - - + +
113A CYS* 3.7 11.4 - - - -
129A MSE 3.4 31.2 - - + -
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Residues in contact with GLN 101 (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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97A LYS* 3.2 34.7 + - + +
98A GLU* 3.9 15.2 - - - +
99A LEU 3.3 0.8 - - - -
100A LEU* 1.3 76.3 - - - +
102A LYS* 1.3 61.8 + - + +
103A ALA 3.6 0.3 + - - -
104A PRO* 3.6 13.5 - - - +
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Residues in contact with LYS 102 (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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61A TYR* 4.0 11.9 + - - -
67A LYS* 3.4 30.6 + - - +
69A SER 5.1 2.0 - - - +
72A SER* 3.8 17.6 + - - -
73A SER* 3.3 29.2 + - - +
98A GLU* 3.6 20.4 + - - +
99A LEU* 3.2 14.3 + - - +
101A GLN* 1.3 78.6 - - + +
103A ALA* 1.3 59.6 + - + +
104A PRO* 3.8 2.3 - - - +
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Residues in contact with ALA 103 (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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99A LEU 3.7 5.7 + - - +
100A LEU* 3.3 13.0 + - - +
101A GLN 3.3 0.2 - - - -
102A LYS* 1.3 81.2 - - + +
104A PRO* 1.4 66.3 - - - +
105A ASN 3.3 3.1 - - - -
106A ASN* 3.2 35.7 + - + +
109A CSX 4.3 6.1 - - - +
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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