Contacts of the helix formed by residues 99 - 117 (chain A) in PDB entry 3MXW
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ILE* 6.1 0.2 - - + -
75A GLU* 5.0 4.9 - - + +
76A LEU* 4.0 10.5 - - + -
77A THR* 6.0 0.2 - - - -
98A MET* 1.3 76.7 - - - +
100A GLN* 1.3 64.7 + - - +
102A CYS* 3.2 21.7 + - - +
103A LYS* 3.0 22.4 + - - +
142A GLU 3.8 10.5 - - - +
143A GLY 2.9 20.0 + - - +
144A ARG* 3.8 19.0 - - + +
185A VAL* 3.7 10.2 - - - +
186A LYS 5.1 0.6 + - - -
188A GLU* 3.5 25.5 + - + +
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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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75A GLU 5.4 2.2 + - - -
77A THR* 4.6 12.4 - - + +
98A MET 4.0 0.2 + - - -
99A THR* 1.3 74.0 - - - +
101A ARG* 1.3 58.2 + - - +
103A LYS* 3.2 27.2 + - - +
104A ASP* 3.0 59.9 + - - +
107A ASN* 5.9 0.6 - - - +
188A GLU* 3.6 16.3 + - - +
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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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1A SO4 3.0 47.6 + - - -
100A GLN* 1.3 76.8 - - - +
102A CYS* 1.3 63.7 + - - +
104A ASP* 3.3 9.0 + - + +
105A LYS* 3.1 40.0 + - - +
169A GLY 4.4 0.6 + - - -
171A ASP* 2.8 39.8 + - - -
185A VAL* 3.8 13.7 - - + -
186A LYS* 3.7 26.1 - - - +
188A GLU* 2.9 21.8 + - - +
191A VAL* 3.9 34.0 - - + +
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Residues in contact with CYS 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 MET* 3.9 18.6 - - + -
99A THR* 3.2 23.4 + - - +
101A ARG* 1.3 77.8 - - - +
103A LYS* 1.3 57.3 + - - +
105A LYS* 3.5 0.7 + - - -
106A LEU* 2.9 31.9 + - - +
143A GLY 3.9 5.6 - - - +
144A ARG 4.4 14.1 - - - -
145A ALA 4.4 2.0 - - - -
146A VAL* 3.9 27.8 - - - -
170A PHE* 4.0 15.4 - - - -
185A VAL* 3.8 15.5 - - + +
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Residues in contact with LYS 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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77A THR* 3.2 45.8 + - + +
78A PRO 2.8 23.0 + - - -
79A ASN* 3.6 25.8 - - - +
98A MET* 3.5 25.9 - - + -
99A THR 3.0 11.5 + - - +
100A GLN* 3.3 30.7 + - - +
102A CYS* 1.3 76.6 - - - +
104A ASP* 1.3 52.2 + - - +
106A LEU 3.3 0.5 + - - -
107A ASN* 2.8 48.5 + - - +
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Residues in contact with ASP 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* 3.0 42.0 + - - +
101A ARG* 3.3 11.8 + - - +
103A LYS* 1.3 76.4 - - - +
105A LYS* 1.3 73.0 + - + +
107A ASN* 3.9 7.9 + - - +
108A ALA* 3.2 21.8 + - - +
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Residues in contact with LYS 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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1A SO4 2.8 34.9 + - - -
101A ARG* 3.1 35.9 + - - +
104A ASP* 1.3 81.2 - - - +
106A LEU* 1.3 59.4 + - - +
108A ALA* 3.4 4.9 + - + +
109A LEU* 3.0 27.7 + - - +
168A ALA* 3.4 24.1 + - - +
169A GLY* 3.4 25.1 - - - +
170A PHE* 3.6 29.5 - - + +
185A VAL* 4.1 11.4 - - + -
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Residues in contact with LEU 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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79A ASN* 3.8 4.5 - - - +
84A ILE* 3.7 22.4 - - + +
86A PHE* 4.3 2.2 - - + -
98A MET* 3.6 32.5 - - + -
102A CYS* 2.9 21.0 + - - +
103A LYS 3.7 3.6 - - - +
105A LYS* 1.3 77.2 - - - +
107A ASN* 1.3 56.9 + - - +
109A LEU* 3.3 2.7 + - + +
110A ALA* 2.9 24.8 + - - +
122A LEU* 3.5 23.1 - - + +
124A VAL* 3.9 14.1 - - + -
146A VAL* 3.7 28.0 - - + -
148A ILE* 4.0 11.4 - - + -
170A PHE* 3.4 11.6 - - + -
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Residues in contact with ASN 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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79A ASN* 3.1 26.0 + - - +
81A ASN* 2.9 29.9 + - - +
84A ILE* 3.8 1.7 - - - +
100A GLN* 5.9 1.0 - - - +
103A LYS* 2.8 35.8 + - - +
104A ASP* 3.9 8.1 + - - +
106A LEU* 1.3 70.4 - - - +
108A ALA* 1.3 65.7 + - - +
110A ALA* 3.3 11.3 + - - +
111A ILE* 3.4 19.3 + - - +
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Residues in contact with ALA 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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104A ASP 3.2 11.4 + - - +
105A LYS* 3.6 9.2 - - - +
107A ASN* 1.3 77.4 - - - +
109A LEU* 1.3 63.3 + - - +
111A ILE* 3.1 22.7 + - - +
112A SER* 3.2 12.6 + - - -
168A ALA* 4.1 20.9 - - + +
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Residues in contact with LEU 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 LYS 3.0 14.7 + - - +
106A LEU* 3.5 10.3 - - + +
107A ASN 3.3 0.2 - - - -
108A ALA* 1.3 74.3 - - - +
110A ALA* 1.3 65.8 + - - +
112A SER* 3.1 8.1 + - - +
113A VAL* 2.9 36.7 + - + +
122A LEU* 3.8 14.4 - - + -
148A ILE* 3.5 32.5 - - + -
161A LEU* 4.3 2.5 - - + +
164A LEU* 3.5 42.0 - - + -
165A ALA* 3.7 13.5 - - + +
168A ALA* 3.7 8.4 - - + +
170A PHE* 4.1 10.3 - - + -
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Residues in contact with ALA 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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81A ASN* 4.1 8.3 - - - +
83A ASP* 4.1 14.5 - - + +
84A ILE* 3.6 33.2 - - + -
106A LEU 2.9 10.3 + - - +
107A ASN 3.5 9.9 - - - +
108A ALA 3.3 0.2 - - - -
109A LEU* 1.3 75.4 - - - +
111A ILE* 1.3 64.0 + - + +
113A VAL* 3.7 2.1 + - - +
114A MET* 3.4 27.3 + - - +
122A LEU* 3.8 13.2 + - + +
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Residues in contact with ILE 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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83A ASP* 6.2 0.2 - - - +
107A ASN 3.4 14.8 + - - +
108A ALA* 3.1 13.7 + - - +
110A ALA* 1.3 80.8 - - + +
112A SER* 1.3 63.8 + - - +
114A MET* 3.4 7.8 + - - +
115A ASN* 3.1 21.5 + - + +
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Residues in contact with SER 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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108A ALA 3.2 4.9 + - - -
109A LEU* 3.1 30.5 + - - +
111A ILE* 1.3 79.0 - - - +
113A VAL* 1.3 59.5 + - - +
115A ASN* 3.2 10.1 + - - +
116A GLN* 2.8 31.4 + - - +
164A LEU* 4.0 23.4 + - - +
168A ALA* 5.1 1.4 - - - +
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Residues in contact with VAL 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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109A LEU* 2.9 32.7 + - + +
110A ALA 4.0 4.3 - - - +
112A SER* 1.3 76.3 + - - +
114A MET* 1.3 58.1 + - - +
116A GLN* 3.2 3.1 + - - +
117A TRP* 2.9 43.0 + - + +
120A VAL* 4.2 5.8 - - + +
121A LYS* 3.6 12.1 - - - +
122A LEU* 3.5 31.0 - - + +
150A THR* 4.6 3.4 - - + -
161A LEU* 3.4 30.3 - - + -
164A LEU* 4.2 10.3 - - + -
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Residues in contact with MET 114 (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 ASP* 3.8 40.2 - - - +
110A ALA 3.4 13.2 + - - +
111A ILE* 3.4 9.7 + - - +
113A VAL* 1.3 76.7 - - - +
115A ASN* 1.3 60.2 + - - +
117A TRP 4.2 1.1 - - - -
118A PRO* 3.5 25.2 - - + +
119A GLY 5.9 3.1 - - - +
120A VAL 3.4 22.2 - - - +
121A LYS* 4.2 22.0 - - + -
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Residues in contact with ASN 115 (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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111A ILE* 3.1 16.8 + - + +
112A SER* 3.5 12.2 + - - +
113A VAL 3.2 0.2 - - - -
114A MET* 1.3 74.7 - - - +
116A GLN* 1.3 72.5 + - - +
118A PRO* 4.2 8.5 - - - +
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Residues in contact with GLN 116 (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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39A LEU* 5.2 4.3 - - - +
112A SER 2.8 17.7 + - - +
113A VAL 3.5 4.5 - - - +
115A ASN* 1.3 84.7 + - - +
117A TRP* 1.3 93.2 + - + +
118A PRO* 3.8 5.3 - - - +
160A MET* 4.2 21.5 - - + +
164A LEU* 3.7 27.9 - - + +
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Residues in contact with TRP 117 (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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113A VAL* 2.9 32.7 + - + +
114A MET 3.5 4.6 - - - +
116A GLN* 1.3 101.3 - - + +
118A PRO* 1.3 70.9 - - - +
120A VAL* 2.9 37.9 + - + +
150A THR* 3.8 20.9 - - + -
157A LYS* 3.6 58.4 - - + +
160A MET* 3.8 18.6 - - + -
161A LEU* 3.8 15.9 - - + -
164A LEU* 3.9 16.8 - - + -
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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