Contacts of the helix formed by residues 97 - 113 (chain A) in PDB entry 5UKM
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLU* 1.3 78.7 - - + +
98A GLU* 1.3 63.9 + - - +
99A GLU* 3.5 7.9 + - - +
100A GLU* 3.0 49.6 + - - +
101A ARG* 3.3 16.0 + - - -
460A MET* 6.3 2.5 - - + -
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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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97A THR* 1.3 73.9 - - - +
99A GLU* 1.3 61.6 + - - +
101A ARG* 3.4 30.9 + - - +
102A LEU* 3.2 32.9 + - - +
139A LYS 4.0 16.3 - - - +
140A GLN* 5.6 0.2 - - - -
141A VAL* 3.9 14.7 + - + +
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Residues in contact with GLU 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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97A THR* 3.2 7.4 + - - +
98A GLU* 1.3 75.9 - - - +
100A GLU* 1.3 65.7 + - + +
102A LEU* 3.6 22.5 + - - +
103A VAL* 3.3 41.9 + - + +
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Residues in contact with GLU 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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95A LEU* 3.5 35.0 - - + +
96A GLU* 3.7 10.0 + - - +
97A THR* 3.0 52.3 + - - +
99A GLU* 1.3 76.7 - - + +
101A ARG* 1.3 57.8 + - - +
103A VAL* 3.4 4.5 + - - +
104A CYS* 2.9 31.7 + - - +
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Residues in contact with ARG 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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92A TYR* 3.4 41.7 - - + +
95A LEU* 3.5 24.0 + - + -
96A GLU 3.2 24.5 + - - -
97A THR 3.3 12.4 + - - -
98A GLU* 3.6 32.1 - - - +
99A GLU 3.3 0.4 - - - -
100A GLU* 1.3 75.7 - - - +
102A LEU* 1.3 59.2 + - - +
103A VAL 2.9 0.5 + - - -
104A CYS 3.1 0.5 + - - -
105A SER* 2.7 37.0 + - - -
141A VAL* 2.9 31.4 + - + +
142A PRO* 4.5 1.4 - - - +
143A PRO* 4.3 27.6 - - - +
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Residues in contact with LEU 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* 3.2 27.7 + - - +
99A GLU* 3.7 31.4 - - - +
100A GLU 3.5 0.2 - - - -
101A ARG* 1.3 76.0 - - - +
103A VAL* 1.3 62.3 + - + +
105A SER* 3.1 15.7 + - - -
106A ARG* 3.5 22.0 + - - +
136A LEU* 5.5 0.8 - - + +
139A LYS* 3.7 46.9 - - + +
141A VAL* 3.6 22.8 - - + +
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Residues in contact with VAL 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 GLU* 3.3 31.6 + - + +
100A GLU* 3.8 7.6 - - - +
101A ARG 3.1 0.4 - - - -
102A LEU* 1.3 74.8 - - + +
104A CYS* 1.3 67.6 + - - +
105A SER 3.4 0.3 + - - -
106A ARG* 3.4 7.3 + - - +
107A GLU* 3.2 32.4 + - - +
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Residues in contact with CYS 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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88A GLU* 5.0 6.3 - - - -
91A LYS* 5.7 2.0 - - - -
92A TYR* 3.9 13.0 - - + -
95A LEU* 3.4 23.1 - - + -
100A GLU 2.9 17.4 + - - +
101A ARG 3.9 0.9 - - - +
103A VAL* 1.3 77.6 - - - +
105A SER* 1.3 56.9 + - - +
107A GLU* 3.2 15.4 + - - +
108A ILE* 2.9 47.7 + - - +
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Residues in contact with SER 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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92A TYR* 3.6 21.2 - - - -
101A ARG 2.7 25.1 + - - -
102A LEU 3.1 7.8 + - - -
104A CYS* 1.3 73.7 - - - +
106A ARG* 1.3 59.0 + - - +
108A ILE* 3.4 3.6 + - - +
109A PHE* 2.9 26.3 + - - +
136A LEU* 3.3 20.4 - - - +
141A VAL* 3.3 17.8 - - - +
145A LEU* 4.0 1.3 - - - -
146A PHE* 3.7 19.5 - - - -
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Residues in contact with ARG 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 LEU* 3.8 23.6 + - - +
103A VAL* 3.4 6.7 + - - +
104A CYS 3.3 0.4 - - - -
105A SER* 1.3 77.6 + - - +
107A GLU* 1.3 59.1 + - - +
109A PHE* 4.0 7.2 - - + -
110A ASP* 2.9 47.5 + - - +
136A LEU* 4.2 15.8 + - + +
139A LYS* 4.8 19.4 - - - +
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Residues in contact with GLU 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 VAL* 3.2 25.3 + - - +
104A CYS* 3.2 18.4 + - - +
106A ARG* 1.3 77.7 - - - +
108A ILE* 1.3 60.5 + - + +
110A ASP* 3.9 2.9 + - - +
111A THR* 3.2 31.4 + - - +
112A TYR* 5.2 0.3 - - - -
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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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85A PHE* 3.6 24.2 - - + -
88A GLU* 3.7 33.4 - - + +
89A ILE 4.6 1.3 - - - +
92A TYR* 3.9 18.2 - - + -
104A CYS* 2.9 38.1 + - - +
105A SER 3.6 6.7 - - - +
107A GLU* 1.3 74.3 - - + +
109A PHE* 1.3 66.9 + - - +
112A TYR* 3.1 27.3 + - + +
113A ILE* 3.9 2.1 + - - +
146A PHE* 3.3 37.2 - - + -
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Residues in contact with PHE 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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105A SER 2.9 17.6 + - - +
106A ARG* 3.6 6.7 - - + +
107A GLU 3.4 0.2 - - - -
108A ILE* 1.3 76.3 - - - +
110A ASP* 1.3 77.1 + - - +
113A ILE* 3.1 54.4 + - + +
114A MET* 3.2 26.8 + - + -
129A ILE* 4.9 4.3 - - + -
132A VAL* 3.8 13.9 - - + -
133A GLN* 3.9 44.2 - - + -
136A LEU* 3.7 25.8 - - + -
146A PHE* 4.7 0.4 - - - -
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Residues in contact with ASP 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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106A ARG* 2.9 40.6 + - - +
107A GLU* 4.6 3.4 - - - +
108A ILE 3.5 0.2 - - - -
109A PHE* 1.3 86.5 - - - +
111A THR* 1.3 59.6 + - - +
114A MET* 3.7 16.4 - - + +
115A LYS* 3.5 19.6 + - - +
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Residues in contact with THR 111 (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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107A GLU* 3.2 20.4 + - - +
109A PHE 3.2 0.6 - - - -
110A ASP* 1.3 80.4 - - - +
112A TYR* 1.3 93.1 + - + +
113A ILE 3.5 0.4 - - - -
115A LYS* 3.2 45.6 - - + +
116A GLU 3.9 0.2 + - - -
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Residues in contact with TYR 112 (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 PRO* 4.1 6.3 - - + -
84A GLU* 3.9 28.9 + - + +
85A PHE* 3.7 56.5 - + + -
88A GLU* 3.5 36.4 + - + -
108A ILE* 3.1 23.8 + - + +
111A THR* 1.3 100.4 - - + +
113A ILE* 1.3 61.2 + - - +
115A LYS* 4.6 8.5 - - - -
116A GLU* 3.2 25.0 - - - +
122A HIS* 3.1 20.4 + - - -
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Residues in contact with ILE 113 (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 PHE* 4.4 5.8 - - + -
108A ILE 4.3 1.6 - - - +
109A PHE* 3.1 58.3 + - + +
112A TYR* 1.3 83.7 - - - +
114A MET* 1.3 61.0 + - - +
115A LYS 3.5 0.2 - - - -
116A GLU* 3.7 2.1 + - - +
117A LEU* 2.9 51.2 + - + +
122A HIS* 3.7 6.2 - - + +
129A ILE* 4.4 7.9 - - + -
132A VAL* 4.3 10.5 - - + -
146A PHE* 4.6 7.9 - - + -
149A TYR* 3.7 41.5 - - + +
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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