Contacts of the helix formed by residues 91 - 110 (chain A) in PDB entry 3UC5
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.8 2.5 - - - +
90A ARG* 1.3 92.8 + - + +
92A GLY* 1.3 60.2 + - - +
93A THR* 3.4 11.7 + - - -
94A ASP* 3.1 25.9 + - - +
95A PHE* 2.9 26.7 + - - +
123A SER* 4.9 5.2 - - - +
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Residues in contact with GLY 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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91A THR* 1.3 74.6 - - - +
93A THR* 1.3 56.8 + - - +
95A PHE* 3.3 10.4 + - - +
96A GLU* 3.0 34.2 + - - +
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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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91A THR* 3.1 10.7 + - - +
92A GLY* 1.3 74.5 - - - +
94A ASP* 1.3 68.9 + - - +
96A GLU* 3.4 5.8 + - - +
97A TYR* 3.1 26.8 + - + +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.9 11.4 - - + -
90A ARG* 2.8 66.4 + - - +
91A THR* 3.1 18.5 + - - +
93A THR* 1.3 81.4 - - - +
95A PHE* 1.3 58.1 + - - +
97A TYR* 4.6 4.7 - - - -
98A GLU* 2.8 38.7 + - + +
1440A ATP 4.0 10.2 + - - +
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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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89A LEU* 4.0 28.7 - - + +
91A THR 2.9 13.1 + - - +
92A GLY* 3.5 13.2 - - - +
93A THR 3.2 0.4 - - - -
94A ASP* 1.3 78.6 - - - +
96A GLU* 1.3 68.5 + - + +
99A LEU* 2.8 63.3 + - + +
115A PHE* 5.8 7.2 - + - -
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Residues in contact with GLU 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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92A GLY 3.0 19.1 + - - +
93A THR* 4.0 5.4 - - - +
94A ASP 3.3 0.2 - - - -
95A PHE* 1.3 88.9 - - + +
97A TYR* 1.3 63.0 + - - +
99A LEU* 3.7 5.5 - - - +
100A GLN* 3.2 22.7 + - - +
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Residues in contact with TYR 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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87A LYS* 4.6 1.5 + - - -
93A THR* 3.1 19.8 + - + +
94A ASP* 3.8 4.7 - - - +
96A GLU* 1.3 77.8 - - - +
98A GLU* 1.3 86.2 + - + +
100A GLN* 3.3 14.5 + - - +
101A MET* 3.2 67.5 + - + +
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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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87A LYS* 2.8 42.8 + - - +
88A GLY 4.7 1.3 - - - +
89A LEU* 3.8 16.8 - - + -
94A ASP* 2.8 27.8 + - + +
95A PHE* 4.1 0.7 - - + +
97A TYR* 1.3 88.8 - - + +
99A LEU* 1.3 60.2 + - - +
101A MET* 3.8 7.0 - - - +
102A ALA* 2.8 32.7 + - - +
115A PHE* 3.4 19.6 - - + -
1440A ATP 3.0 28.9 + - - -
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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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95A PHE* 2.8 47.9 + - + +
96A GLU* 3.7 6.7 - - - +
98A GLU* 1.3 77.1 - - - +
100A GLN* 1.3 65.6 + - + +
102A ALA* 3.3 5.6 + - + +
103A GLN* 3.0 67.0 + - + +
115A PHE* 4.3 9.8 - - + -
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Residues in contact with GLN 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 GLU 3.2 10.9 + - - +
97A TYR* 3.6 18.5 + - - +
98A GLU 3.3 0.2 - - - -
99A LEU* 1.3 84.3 - - + +
101A MET* 1.3 65.0 + - - +
103A GLN* 3.3 5.9 + - - +
104A MET* 2.9 33.9 + - + +
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Residues in contact with MET 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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73A VAL* 6.5 1.1 - - + -
87A LYS* 3.2 31.2 - - + +
97A TYR* 3.2 56.6 + - + +
98A GLU* 3.3 5.8 + - - +
100A GLN* 1.3 83.4 - - + +
102A ALA* 1.3 58.5 + - - +
104A MET* 3.3 6.9 + - - +
105A ASN* 2.8 46.7 + - - +
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Residues in contact with ALA 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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98A GLU 2.8 18.3 + - - +
99A LEU* 3.8 5.4 - - + +
101A MET* 1.3 78.3 - - - +
103A GLN* 1.3 58.2 + - + +
105A ASN* 3.3 3.2 + - - +
106A LYS* 2.9 30.5 + - - +
111A VAL 4.6 1.7 - - - +
113A THR* 3.8 33.8 + - + +
115A PHE* 3.8 13.7 - - + -
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Residues in contact with GLN 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* 3.0 53.8 + - + +
100A GLN* 3.9 6.3 - - - +
102A ALA* 1.3 73.7 - - + +
104A MET* 1.3 65.6 + - - +
106A LYS* 3.8 6.0 - - - +
107A HIS* 2.9 24.4 + - - +
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Residues in contact with MET 104 (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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100A GLN* 2.9 23.0 + - + +
101A MET* 3.6 7.4 - - - +
103A GLN* 1.3 78.2 - - - +
105A ASN* 1.3 59.9 + - - +
107A HIS* 3.2 13.0 + - - +
108A ILE* 3.0 51.8 + - + +
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Residues in contact with ASN 105 (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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72A LEU* 5.5 3.1 - - - +
73A VAL* 5.0 8.2 + - - +
74A VAL* 3.5 28.6 + - + +
85A ILE* 4.0 19.7 - - + +
101A MET* 2.8 37.7 + - - +
102A ALA* 3.7 7.2 - - - +
104A MET* 1.3 74.5 - - - +
106A LYS* 1.3 64.3 + - - +
108A ILE* 3.7 16.1 - - - +
109A ALA 3.2 18.2 + - - -
110A GLY 3.6 3.3 + - - -
111A VAL 3.8 11.6 + - - +
113A THR* 4.9 1.5 + - - +
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Residues in contact with LYS 106 (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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102A ALA 2.9 16.1 + - - +
103A GLN* 3.8 6.7 - - - +
105A ASN* 1.3 76.5 - - - +
107A HIS* 1.3 60.7 + - - +
110A GLY* 2.9 44.3 + - - -
111A VAL 3.5 14.7 + - - +
112A ASP* 2.8 37.2 + - - +
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Residues in contact with HIS 107 (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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103A GLN 2.9 17.9 + - - +
104A MET* 3.2 14.3 + - - +
106A LYS* 1.3 81.5 - - - +
108A ILE* 1.3 78.5 + - + +
110A GLY 4.7 0.2 + - - -
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Residues in contact with ILE 108 (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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72A LEU* 4.3 21.5 - - + -
74A VAL* 3.9 25.4 - - + -
78A ARG* 4.4 6.6 + - - -
104A MET* 3.0 39.0 + - + +
105A ASN* 3.7 19.5 - - - +
107A HIS* 1.3 91.7 - - + +
109A ALA* 1.3 60.6 + - + +
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Residues in contact with ALA 109 (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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74A VAL* 3.6 25.8 - - + -
78A ARG* 3.3 52.9 + - - +
105A ASN 3.2 6.6 + - - +
107A HIS 3.4 0.6 - - - -
108A ILE* 1.3 78.6 - - - +
110A GLY* 1.3 64.8 + - - +
111A VAL* 3.3 3.3 + - + +
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Residues in contact with GLY 110 (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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105A ASN 3.6 0.2 + - - -
106A LYS* 2.9 41.8 + - - -
107A HIS 4.7 0.4 + - - -
109A ALA* 1.3 77.0 - - - +
111A VAL* 1.3 61.6 + - - +
112A ASP* 3.7 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