Contacts of the helix formed by residues 107 - 122 (chain A) in PDB entry 4MHV
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 SER 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU 3.8 1.2 + - - -
106A TRP* 1.3 75.0 - - - +
108A GLU* 1.3 64.2 + - - +
109A GLN* 3.3 10.9 + - - +
110A GLN* 3.1 37.5 + - - +
111A VAL* 3.1 22.3 + - - +
135A ASN* 4.3 6.1 - - - +
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Residues in contact with GLU 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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107A SER* 1.3 72.0 - - - +
109A GLN* 1.4 56.3 + - - +
111A VAL* 3.6 4.3 + - - +
112A CYS* 3.2 23.6 + - - +
132A PHE 4.7 1.7 - - - +
133A GLY* 3.7 28.5 - - - +
134A MET* 3.2 31.6 - - - +
135A ASN* 4.2 4.9 - - - +
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Residues in contact with GLN 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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107A SER* 3.1 9.6 + - - +
108A GLU* 1.4 75.1 - - - +
110A GLN* 1.4 54.3 + - + +
112A CYS* 3.1 11.0 + - + +
113A GLN* 2.8 52.2 + - - +
120B ASN* 3.1 38.1 + - - +
123B SER* 4.8 12.6 - - - +
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Residues in contact with GLN 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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97A LEU 4.6 2.4 + - - -
98A GLY 3.2 26.5 + - - -
99A ILE* 3.8 12.7 - - + +
100A PRO* 3.4 22.9 - - - +
105A LEU 4.3 1.7 - - - +
106A TRP* 3.4 18.6 - - + -
107A SER* 3.1 36.8 + - - +
109A GLN* 1.4 73.3 - - + +
111A VAL* 1.4 63.8 + - - +
113A GLN* 3.4 22.0 + - - +
114A TRP* 3.1 23.7 + - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 4.1 16.6 - - + -
107A SER 3.1 11.6 + - - +
108A GLU 3.6 3.1 - - - +
109A GLN 3.3 0.2 - - - -
110A GLN* 1.4 75.1 - - - +
112A CYS* 1.4 61.4 + - - +
114A TRP* 3.2 7.7 + - + +
115A LEU* 3.2 31.9 + - + +
132A PHE* 3.8 20.2 - - + +
134A MET* 3.3 24.5 - - + +
135A ASN 3.8 3.6 - - - +
136A GLY* 3.7 22.2 - - - +
139A LEU* 4.1 26.7 - - + -
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Residues in contact with CYS 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 GLU 3.2 10.3 + - - +
109A GLN* 3.1 13.8 + - - +
111A VAL* 1.4 77.5 - - - +
113A GLN* 1.4 51.7 + - - +
115A LEU* 3.1 6.8 + - - +
116A LEU* 2.8 55.8 + - - +
129A LEU* 4.0 34.3 - - + -
132A PHE 5.2 2.4 + - - +
119B THR* 4.3 10.5 - - - -
120B ASN* 5.3 4.9 - - - -
123B SER* 6.3 1.8 - - - -
124B LEU 5.4 1.3 - - - -
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Residues in contact with GLN 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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90A PHE* 4.9 0.2 - - - -
93A GLU* 5.1 2.6 - - - +
97A LEU* 4.0 36.9 + - + +
99A ILE* 3.4 22.3 - - + +
109A GLN* 2.8 45.7 + - - +
110A GLN* 3.4 30.7 - - - +
111A VAL 3.3 0.4 - - - -
112A CYS* 1.4 71.3 - - - +
114A TRP* 1.4 55.0 + - - +
116A LEU* 3.1 11.2 + - + +
117A TRP* 2.9 29.3 + - - +
120B ASN* 3.3 25.9 + - - +
202B GOL 6.4 0.2 - - - -
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Residues in contact with TRP 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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90A PHE* 3.6 42.5 - + + -
106A TRP* 3.7 20.0 - + + -
110A GLN 3.1 13.3 + - - +
111A VAL* 3.2 8.9 + - + +
113A GLN* 1.4 73.7 - - - +
115A LEU* 1.3 87.5 + - + +
117A TRP* 3.2 8.3 + + - +
118A ALA* 3.2 19.2 + - - +
139A LEU* 4.0 29.2 - - + -
147A PHE* 3.7 26.0 - + - -
159A LEU* 3.5 37.9 - - + +
162A HIS* 3.1 24.9 + + - -
163A LEU* 3.9 19.7 - - + -
166A MET* 3.8 5.8 - - + +
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Residues in contact with LEU 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 VAL* 3.2 19.7 + - + +
112A CYS* 3.1 8.3 + - - +
114A TRP* 1.3 100.1 - - + +
116A LEU* 1.4 53.1 + - - +
118A ALA* 3.6 5.2 + - - +
119A THR* 2.7 36.9 + - - -
127A VAL* 3.6 26.5 - - + +
129A LEU* 4.0 18.4 - - + -
132A PHE* 3.5 46.0 - - + -
147A PHE* 5.3 0.2 - - + -
159A LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 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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112A CYS* 2.8 31.0 + - - +
113A GLN* 3.1 12.5 + - - +
115A LEU* 1.4 74.4 - - - +
117A TRP* 1.4 64.5 + - - +
119A THR* 3.3 6.0 + - - +
120A ASN* 3.1 23.7 + - - +
129A LEU* 4.2 7.9 - - + -
203A ACT 3.9 9.9 - - + -
116B LEU* 3.7 42.9 - - + +
119B THR* 3.8 19.7 - - + -
120B ASN* 3.7 32.8 - - + +
202B GOL 4.7 10.1 - - - +
203B ACT 4.2 2.1 - - - +
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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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86A THR 3.9 17.0 - - - -
87A PHE* 4.2 5.8 - + - -
89A GLY* 3.9 6.5 + - - -
90A PHE* 3.4 53.6 - + + +
93A GLU* 3.7 34.0 + - + +
113A GLN 2.9 12.5 + - - +
114A TRP* 3.2 12.1 + + - +
116A LEU* 1.4 74.8 - - - +
118A ALA* 1.3 71.7 + - + +
120A ASN* 3.3 4.2 + - - +
121A GLU* 2.9 67.3 + - + +
122A PHE* 4.2 20.6 - + - -
159A LEU* 6.3 0.4 - - + -
162A HIS* 3.7 25.6 - + - -
203B ACT 3.7 12.8 - - - -
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Residues in contact with ALA 118 (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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114A TRP* 3.2 15.2 + - - +
115A LEU* 3.8 5.8 - - + +
117A TRP* 1.3 87.2 - - + +
119A THR* 1.3 58.6 + - - +
121A GLU* 4.1 0.4 - - - -
122A PHE* 2.9 48.7 + - + +
124A LEU* 3.6 7.7 - - + +
127A VAL* 5.7 0.2 - - + -
159A LEU* 3.5 31.2 - - + -
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Residues in contact with THR 119 (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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115A LEU 2.7 24.3 + - - -
116A LEU* 3.5 10.2 - - - +
118A ALA* 1.3 73.8 - - - +
120A ASN* 1.3 57.9 + - - +
123A SER* 3.1 9.5 + - - -
124A LEU* 2.8 58.0 + - + +
126A ASN 5.9 0.2 - - - +
127A VAL* 3.5 18.7 - - - +
203A ACT 4.5 6.8 + - - +
109B GLN* 4.6 1.0 - - - +
112B CYS* 4.4 2.9 - - - -
116B LEU* 3.8 13.9 - - + +
129B LEU* 3.6 21.3 - - + -
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Residues in contact with ASN 120 (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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116A LEU 3.1 5.4 + - - +
117A TRP 3.7 6.2 - - - +
119A THR* 1.3 76.9 - - - +
121A GLU* 1.3 70.6 + - - +
123A SER* 3.4 12.0 + - - -
97B LEU* 4.9 4.2 - - - +
109B GLN* 2.9 37.1 + - - +
113B GLN* 3.3 33.3 + - - +
116B LEU* 3.8 8.4 - - + +
203B ACT 3.8 35.4 - - + +
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Residues in contact with GLU 121 (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 THR* 4.2 14.8 + - - +
89A GLY* 5.6 2.0 - - - -
117A TRP* 2.9 59.1 + - + +
118A ALA* 3.9 6.3 - - - +
120A ASN* 1.3 79.1 + - - +
122A PHE* 1.3 80.9 + - + +
123A SER* 3.6 1.4 + - - -
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Residues in contact with PHE 122 (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 LEU* 5.0 7.2 - - + -
86A THR* 3.4 33.7 - - + -
87A PHE* 4.0 20.6 - + - -
117A TRP* 4.2 20.2 - + - -
118A ALA* 2.9 32.1 + - + +
119A THR 4.0 0.2 - - - -
121A GLU* 1.3 88.5 - - + +
123A SER* 1.3 70.8 + - - +
124A LEU* 3.6 20.5 - - + +
155A VAL* 6.0 2.2 - - + -
158A ILE* 4.0 26.7 - - + -
159A LEU* 5.4 1.8 - - + -
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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