Contacts of the helix formed by residues 107 - 122 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU 3.8 0.8 + - - -
106B TRP* 1.4 75.4 - - - +
108B GLU* 1.3 64.2 + - - +
109B GLN* 3.3 10.0 + - - +
110B GLN* 3.1 37.0 + - - +
111B VAL* 3.1 22.3 + - - +
135B ASN* 4.3 8.3 - - - +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B SER* 1.3 72.8 - - - +
109B GLN* 1.4 55.3 + - - +
111B VAL* 3.6 4.7 + - - +
112B CYS* 3.2 23.2 + - - +
132B PHE 4.7 2.1 - - - +
133B GLY* 3.7 23.2 - - - +
134B MET* 3.2 33.1 + - - +
135B ASN* 4.2 5.5 + - + +
201B GOL 3.5 16.4 + - - -
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR 4.6 1.0 - - - +
120A ASN* 2.9 40.9 + - - +
123A SER* 2.7 35.6 + - - +
107B SER* 3.2 9.0 + - - +
108B GLU* 1.4 74.9 - - - +
110B GLN* 1.3 53.6 + - + +
112B CYS* 3.1 20.5 + - - +
113B GLN* 2.8 44.8 + - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU 4.6 3.0 + - - -
98B GLY 3.2 26.5 + - - -
99B ILE* 3.8 12.8 - - + +
100B PRO* 3.4 21.5 - - - +
105B LEU 4.3 1.6 - - - +
106B TRP* 3.4 18.7 - - + -
107B SER* 3.1 37.5 + - - +
109B GLN* 1.3 72.6 - - + +
111B VAL* 1.4 64.0 + - - +
113B GLN* 3.3 22.8 - - - +
114B TRP* 3.1 22.9 + - - +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TRP* 4.1 17.0 - - + -
107B SER 3.1 11.4 + - - +
108B GLU 3.6 3.6 - - - +
109B GLN 3.3 0.2 - - - -
110B GLN* 1.4 75.2 - - - +
112B CYS* 1.4 61.9 + - - +
114B TRP* 3.2 7.2 + - + +
115B LEU* 3.2 32.3 + - + +
132B PHE* 3.8 20.4 - - + +
134B MET* 3.3 24.9 - - + +
135B ASN 3.8 2.9 - - - +
136B GLY* 3.8 23.1 - - - +
139B LEU* 4.1 27.8 - - + -
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Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 4.4 4.7 - - - -
123A SER* 6.2 0.4 - - - -
124A LEU 4.4 9.4 - - - -
125A VAL* 6.1 0.9 - - + -
108B GLU 3.2 10.9 + - - +
109B GLN* 3.1 26.3 + - - +
111B VAL* 1.4 75.6 - - - +
113B GLN* 1.4 56.4 + - - +
115B LEU* 3.1 6.5 + - - +
116B LEU* 2.9 50.9 + - - +
129B LEU* 4.1 32.3 - - + -
132B PHE 5.2 2.2 + - - +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASN* 3.3 31.3 + - - +
90B PHE* 4.9 0.4 - - - -
93B GLU* 5.1 2.6 - - - +
97B LEU* 4.0 41.0 + - + +
99B ILE* 3.4 21.5 - - + +
109B GLN* 2.8 27.6 + - - +
110B GLN* 3.3 31.0 - - - +
112B CYS* 1.4 71.0 - - - +
114B TRP* 1.4 57.3 + - - +
116B LEU* 3.1 10.3 + - - +
117B TRP* 2.9 29.5 + - - +
203B ACT 5.1 1.3 - - + -
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Residues in contact with TRP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.6 41.1 - + + -
106B TRP* 3.7 24.7 - + + -
110B GLN 3.1 13.5 + - - +
111B VAL* 3.2 9.4 + - + +
113B GLN* 1.4 72.4 - - - +
115B LEU* 1.3 88.4 + - + +
117B TRP* 3.2 6.9 + + - +
118B ALA* 3.2 19.9 + - - +
132B PHE* 5.4 0.2 - + - -
139B LEU* 4.0 28.3 - - + -
147B PHE* 3.7 25.8 - + - -
159B LEU* 3.4 39.1 - - + +
162B HIS* 3.1 26.2 + + - -
163B LEU* 3.9 19.1 - - + -
166B MET* 4.5 1.7 - - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 3.2 17.9 + - + +
112B CYS* 3.1 7.3 + - - +
114B TRP* 1.3 101.8 - - + +
116B LEU* 1.4 53.3 + - - +
118B ALA* 3.7 4.6 + - - +
119B THR* 2.7 36.5 + - - -
127B VAL* 4.1 15.2 - - + +
129B LEU* 4.0 22.2 - - + -
132B PHE* 3.5 48.0 - - + -
159B LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 116 (chain B).
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* 3.7 42.5 - - + +
119A THR* 3.8 19.3 - - + -
120A ASN* 3.8 32.3 - - + +
203A ACT 3.8 13.0 - - + -
112B CYS* 2.9 30.6 + - - +
113B GLN* 3.6 9.9 - - - +
115B LEU* 1.4 74.4 - - - +
117B TRP* 1.4 64.6 + - - +
119B THR* 3.4 5.5 + - - -
120B ASN* 3.1 19.4 + - - +
129B LEU* 4.2 6.7 - - + -
202B GOL 4.0 3.4 - - - +
203B ACT 3.9 15.5 - - + -
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Residues in contact with TRP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR 4.1 13.7 - - - -
87B PHE* 4.2 6.3 - - - -
89B GLY 3.9 7.6 + - - -
90B PHE* 3.4 56.0 - + + +
93B GLU* 3.6 26.2 + - + +
113B GLN 2.9 12.7 + - - +
114B TRP* 3.5 9.6 - + - +
116B LEU* 1.4 76.3 - - - +
118B ALA* 1.3 79.3 + - + +
120B ASN* 3.3 4.7 + - - +
121B GLU* 2.9 70.9 + - + +
122B PHE* 4.2 13.5 - + - -
162B HIS* 3.6 26.7 - + - -
202B GOL 3.6 31.2 + - - -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TRP* 3.2 14.8 + - - +
115B LEU* 3.8 5.4 - - - +
117B TRP* 1.3 92.7 - - + +
119B THR* 1.4 56.9 + - - +
121B GLU* 4.2 0.2 - - - -
122B PHE* 2.9 43.5 + - + -
124B LEU* 3.5 9.7 - - + +
159B LEU* 3.6 31.9 - - + -
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Residues in contact with THR 119 (chain B).
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* 4.3 5.4 - - - -
116A LEU* 3.8 13.7 - - + -
129A LEU* 3.6 24.5 - - + -
203A ACT 4.2 2.4 - - - +
115B LEU 2.7 24.0 + - - -
116B LEU* 3.5 10.0 - - - -
117B TRP 3.4 0.2 - - - -
118B ALA* 1.4 71.8 - - - +
120B ASN* 1.3 58.2 + - - +
123B SER* 3.0 10.2 + - - -
124B LEU* 3.0 52.9 + - - +
127B VAL* 3.1 24.1 - - + +
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Residues in contact with ASN 120 (chain B).
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* 4.8 3.4 - - - +
109A GLN* 3.1 38.3 + - - +
112A CYS* 5.3 4.2 - - - -
113A GLN* 3.3 29.7 + - - +
116A LEU* 3.7 19.1 - - + +
116B LEU 3.1 8.5 + - - +
117B TRP 3.7 6.1 - - - +
119B THR* 1.3 76.9 - - - +
121B GLU* 1.3 65.8 + - - +
122B PHE 3.4 0.5 + - - -
123B SER* 3.4 15.1 + - - -
202B GOL 3.2 29.0 + - - -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 4.6 12.1 - - - +
89B GLY* 5.5 3.3 - - - -
117B TRP* 2.9 61.7 + - + +
118B ALA* 3.8 5.6 - - - +
120B ASN* 1.3 74.6 + - - +
122B PHE* 1.3 78.6 + - + +
123B SER* 5.1 0.5 + - - -
202B GOL 4.0 10.6 + - - -
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 3.6 26.0 - - + -
86B THR* 3.4 25.4 - - - -
87B PHE* 3.8 22.7 - + - -
117B TRP* 4.2 21.1 - + - -
118B ALA* 2.9 30.0 + - + +
121B GLU* 1.3 94.3 - - + +
123B SER* 1.4 71.9 + - - +
124B LEU* 3.3 22.8 + - + +
158B ILE* 4.1 24.2 - - + -
159B LEU* 5.5 0.9 - - + -
162B HIS* 5.9 0.4 - - - -
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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