Contacts of the helix formed by residues 87 - 107 (chain A) in PDB entry 1U5T
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASN 4.9 2.4 + - - -
55A GLN* 3.6 36.5 + - - +
83A LYS 5.4 0.7 - - - +
84A HIS* 4.3 14.3 + - - +
85A LEU 2.8 3.6 + - - -
86A PHE* 1.3 81.3 - - + +
88A VAL* 1.3 71.5 + - - +
89A ASN 3.0 1.3 - - - -
90A ASP* 3.5 15.3 - - + +
91A PHE* 3.3 17.3 + - - +
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Residues in contact with VAL 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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51A ASN 5.3 2.0 - - - +
54A LEU* 3.8 48.2 - - + +
55A GLN* 4.2 8.7 - - + +
61A ARG* 5.3 3.6 - - + -
65A MET* 4.9 0.7 - - + -
79A PHE* 3.0 40.6 - - + -
85A LEU* 3.0 18.6 + - + +
87A THR* 1.3 85.0 + - - +
89A ASN* 1.3 60.9 + - - +
91A PHE* 3.3 11.5 - - - +
92A TYR* 3.1 30.6 + - + -
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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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76A LEU* 2.8 49.5 + - - +
79A PHE* 3.4 27.5 - - - +
80A ASP* 4.5 2.9 - - - +
85A LEU 4.1 0.6 + - - -
86A PHE* 4.3 17.8 - - + +
87A THR 3.0 0.4 - - - +
88A VAL* 1.3 76.5 - - - +
90A ASP* 1.3 68.6 + - - +
92A TYR* 2.6 7.6 + - - -
93A TYR* 2.6 57.7 + - + -
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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
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86A PHE* 3.8 14.0 + - - +
87A THR* 3.4 22.1 + - - +
88A VAL 3.4 0.6 - - - -
89A ASN* 1.3 77.3 - - - +
91A PHE* 1.3 52.5 + - - +
93A TYR* 3.0 8.1 + - - +
94A GLU* 2.4 44.4 + - + +
399B GLU* 5.0 1.2 - - - +
450B ILE 5.7 0.7 - - - +
453B GLY* 5.5 0.5 - - - -
454B LEU* 3.6 41.4 + - - +
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Residues in contact with PHE 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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55A GLN* 5.0 10.3 - - - +
61A ARG* 2.7 48.9 - - - -
87A THR 3.3 9.5 + - - +
88A VAL* 3.3 14.8 - - - +
90A ASP* 1.3 78.9 - - - +
92A TYR* 1.3 104.6 + + - +
94A GLU* 3.6 9.4 - - - +
95A VAL* 2.8 26.5 + - + +
127A LEU* 4.9 11.2 - - + -
128A ASN 4.3 2.7 - - - -
129A VAL* 3.5 24.9 - - + -
133A ASP* 2.8 15.5 - - + -
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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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61A ARG* 3.2 22.3 - - + +
65A MET* 3.4 33.2 - - + +
76A LEU* 4.4 15.0 - - + -
79A PHE* 5.0 0.2 - + - -
88A VAL* 3.1 29.1 + - + -
89A ASN* 2.6 18.2 + - - +
91A PHE* 1.3 104.0 - + - +
93A TYR* 1.3 67.8 + - + +
95A VAL* 3.1 2.4 + - + +
96A CYS* 3.0 18.0 + - - -
132A ASP 5.4 0.2 - - - -
133A ASP* 3.4 36.5 + - + -
136A LYS* 4.8 14.3 - - + +
137A SER* 3.3 8.1 + - - -
140A MET* 3.5 23.6 - - + -
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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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76A LEU* 3.4 27.5 - - + +
86A PHE* 4.2 17.4 - + - -
89A ASN* 2.6 51.7 + - + -
90A ASP* 3.3 7.6 - - - +
92A TYR* 1.3 69.2 - - - +
94A GLU* 1.3 67.3 + - - +
96A CYS* 2.6 30.1 + - - +
97A LEU* 2.9 9.5 - - + +
140A MET* 3.6 13.0 - - + -
441B TYR* 5.0 0.4 - - - +
454B LEU* 3.8 20.2 - - + -
455B ILE* 3.6 14.4 - - - +
456B SER* 3.3 44.6 - - - +
459B GLU* 4.4 8.8 + - - -
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Residues in contact with GLU 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 ASP* 2.4 39.8 + - + +
91A PHE* 3.6 10.1 - - - +
93A TYR* 1.3 65.1 - - - +
95A VAL* 1.3 65.1 + - - +
97A LEU* 2.8 24.7 + - - +
98A LYS* 3.2 8.7 + - - +
127A LEU* 4.6 19.3 - - + +
454B LEU* 3.7 18.5 - - + +
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Residues in contact with VAL 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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91A PHE* 2.8 22.8 + - + +
92A TYR* 3.9 4.5 - - + +
94A GLU* 1.3 73.7 - - - +
96A CYS* 1.3 65.1 + - - +
98A LYS* 3.1 8.0 + - - +
99A VAL* 3.0 21.3 + - + +
124A PHE* 3.5 25.1 - - + -
127A LEU* 4.7 6.5 - - + +
129A VAL* 3.3 37.9 - - + -
133A ASP* 5.2 1.6 - - + +
134A LEU* 4.5 11.2 - - - +
137A SER* 2.8 32.5 - - - +
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Residues in contact with CYS 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 TYR 3.0 11.4 + - - -
93A TYR* 2.6 21.0 + - - +
95A VAL* 1.3 69.4 - - - +
97A LEU* 1.3 66.5 + - + +
99A VAL* 2.9 10.5 + - - +
100A ILE* 2.8 24.1 + - - +
137A SER* 2.8 29.6 + - - -
140A MET* 3.7 37.5 - - - -
141A LEU* 4.3 15.0 - - + +
441B TYR* 4.8 1.6 - - + +
457B PRO* 4.5 11.9 - - + -
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Residues in contact with LEU 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* 2.9 24.0 - - + +
94A GLU* 2.8 17.2 + - - +
96A CYS* 1.3 72.8 - - + +
98A LYS* 1.3 50.2 + - - +
100A ILE* 3.0 10.0 + - + +
101A GLU* 2.7 36.2 + - - +
441B TYR* 3.6 32.3 - - + +
442B ALA* 3.8 28.7 - - + +
445B ASN* 3.8 21.8 - - + +
446B LYS* 5.0 2.9 - - + +
454B LEU* 4.4 13.2 - - + -
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Residues in contact with LYS 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 GLU 3.2 6.1 + - - +
95A VAL* 3.1 14.8 + - - +
97A LEU* 1.3 75.1 - - - +
99A VAL* 1.3 54.6 + - - +
101A GLU* 2.9 23.4 + - - +
102A ILE* 2.4 54.1 + - + +
123A HIS* 3.7 18.7 + - - +
124A PHE* 3.3 28.0 - - + -
126A LYS* 3.9 30.7 - - - +
127A LEU* 5.8 5.1 - - + +
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Residues in contact with VAL 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 VAL* 3.0 18.0 + - + +
96A CYS* 2.9 8.8 + - - +
98A LYS* 1.3 72.7 - - - +
100A ILE* 1.3 70.6 + - - +
101A GLU 2.9 1.2 + - - -
102A ILE* 4.3 6.3 - - - +
103A CYS* 2.9 28.0 + - - +
119A LEU* 4.1 6.3 - - + -
124A PHE* 3.9 7.0 - - + -
134A LEU* 3.7 29.4 - - + -
137A SER* 5.0 2.0 - - - +
138A ILE* 4.7 6.5 - - + -
141A LEU* 4.2 8.1 - - + -
147A PHE* 3.7 22.9 - - + -
158A LEU* 3.7 21.8 - - + -
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Residues in contact with ILE 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 CYS 2.8 19.1 + - - +
97A LEU* 3.2 14.4 - - - +
99A VAL* 1.3 76.1 - - - +
101A GLU* 1.3 60.0 + - - +
103A CYS* 3.6 3.8 - - - +
104A ARG* 3.5 20.2 + - - +
141A LEU* 3.3 30.7 - - + -
144A LEU* 3.6 5.6 - - + -
146A CYS* 4.9 0.2 - - - -
147A PHE* 3.6 17.6 - - + -
438B VAL* 3.0 48.0 - - + +
439B ASP* 5.6 2.0 - - - +
441B TYR* 4.6 7.4 - - + -
442B ALA* 4.5 14.6 - - + -
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Residues in contact with GLU 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 LEU 2.7 12.4 + - - +
98A LYS* 2.9 28.4 + - - +
99A VAL 2.9 0.2 + - - -
100A ILE* 1.3 74.5 - - - +
102A ILE* 1.3 70.4 + - - +
103A CYS 2.9 1.3 - - - -
104A ARG* 2.7 33.5 + - - +
105A GLN* 2.8 45.1 + - + +
446B LYS* 5.8 9.0 - - - +
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Residues in contact with ILE 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 LYS* 2.4 60.9 + - + +
99A VAL* 4.2 2.5 - - - +
101A GLU* 1.3 70.4 - - - +
103A CYS* 1.3 57.7 + - - +
105A GLN* 3.5 8.7 + - - +
106A THR* 2.4 34.9 + - - +
114A ILE* 6.0 0.7 - - + -
119A LEU* 4.2 16.6 - - + -
123A HIS* 3.0 69.1 - - + +
124A PHE* 4.1 18.4 - - + -
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Residues in contact with CYS 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 VAL* 2.9 22.1 + - - +
100A ILE 3.6 5.8 - - - +
101A GLU 2.7 3.4 + - - -
102A ILE* 1.3 78.0 - - - +
104A ARG* 1.3 62.6 + - - +
106A THR* 3.0 11.0 + - - -
107A LYS* 3.2 11.1 + - - +
110A ASN* 4.8 0.2 - - - +
114A ILE* 4.3 15.3 - - - -
119A LEU* 5.4 4.3 - - - -
147A PHE* 4.5 13.5 - - + -
158A LEU* 3.9 30.5 - - - -
160A SER* 3.5 32.9 + - - +
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Residues in contact with ARG 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 ILE* 3.5 12.1 + - - +
101A GLU* 2.7 28.8 + - + +
103A CYS* 1.3 70.2 - - - +
105A GLN* 1.3 54.8 + - - +
106A THR 2.3 19.4 + - - -
107A LYS* 3.0 20.2 + - + +
160A SER* 5.9 1.1 - - - -
439B ASP* 4.3 17.9 + - - -
442B ALA* 5.3 10.7 - - - +
446B LYS* 5.1 10.3 - - - +
529B LEU* 5.1 23.6 - - + -
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Residues in contact with GLN 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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101A GLU* 2.8 47.9 + - + +
102A ILE* 4.1 7.6 - - - +
104A ARG* 1.3 74.0 - - - +
106A THR* 1.3 58.0 + - - +
109A MET* 5.8 0.2 - - - +
123A HIS* 5.8 6.5 + - - -
25C GLN* 5.3 7.1 + - - +
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Residues in contact with THR 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 ILE* 2.4 33.8 + - - +
103A CYS* 3.0 4.5 + - - -
104A ARG 2.3 17.2 + - - -
105A GLN* 1.3 73.0 + - - +
107A LYS* 1.3 49.7 - - - -
108A ASP 2.2 24.1 + - - -
109A MET* 2.5 36.8 + - + +
110A ASN* 2.8 32.9 - - + +
114A ILE* 5.2 8.2 - - + +
118A GLU* 4.8 13.0 - - - +
123A HIS* 4.6 6.6 + - + +
25C GLN* 6.3 0.4 - - - -
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Residues in contact with LYS 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 CYS 3.2 9.8 + - - +
104A ARG* 3.0 15.0 + - + +
106A THR* 1.3 72.2 - - - +
108A ASP* 1.3 85.2 + - - +
110A ASN* 3.5 7.8 + - - -
111A GLY* 3.6 20.8 + - - -
112A GLY* 4.3 9.4 - - - +
160A SER* 5.5 4.3 - - - -
161A VAL* 4.7 16.5 - - + +
511B LEU* 4.4 6.8 - - - +
529B LEU* 4.2 12.8 - - + -
533B MET* 3.3 41.4 - - + -
21C LEU* 3.6 19.7 - - - +
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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