Contacts of the helix formed by residues 102 - 121 (chain A) in PDB entry 3MYV
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 TRP 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 4.3 8.0 - - + +
100A SER 3.1 0.2 - - - -
101A LEU* 1.3 80.0 - - - +
103A GLY* 1.3 73.5 + - - +
104A ARG 3.4 0.6 + - - -
105A PRO* 3.6 2.3 - - - +
106A PHE* 3.2 55.3 + + + -
150A LEU* 3.9 2.0 - - - +
154A PHE* 3.7 35.2 - + + -
168A ALA* 4.5 2.5 - - + -
169A PRO* 3.4 27.6 - - + -
460A ILE* 3.7 36.3 - - + -
461A PRO* 3.6 30.3 - - + -
464A GLN* 3.5 42.8 + - + +
471A MSE 5.1 1.6 - - - -
506A EDO 3.8 10.3 + - - -
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Residues in contact with GLY 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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100A SER* 3.3 6.4 + - - +
102A TRP* 1.3 92.1 - - - +
104A ARG* 1.3 57.1 + - - +
106A PHE* 3.4 4.0 + - - +
107A TYR* 2.9 30.1 + - - +
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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
----------------------------------------------------------
51A ASP 5.1 0.4 + - - -
52A LEU* 2.9 63.4 + - - +
55A GLY* 4.1 15.0 - - - -
57A GLY* 5.1 2.0 - - - +
58A TYR* 3.8 20.2 - - + +
100A SER* 2.8 40.8 + - - +
103A GLY* 1.3 68.9 - - - +
105A PRO* 1.4 68.6 - - + +
107A TYR* 3.2 9.0 + - - +
108A ILE* 3.0 38.2 + - + +
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Residues in contact with PRO 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.7 34.1 - - + +
100A SER 3.2 13.5 - - - +
101A LEU* 3.5 19.5 - - + +
102A TRP 3.6 2.2 - - - +
104A ARG* 1.4 89.9 - - + +
106A PHE* 1.3 56.3 + - - +
108A ILE* 3.4 1.6 + - - +
109A LEU* 3.0 34.9 + - - +
146A CYS* 4.0 23.9 - - + +
149A ASP* 5.3 2.7 - - + -
150A LEU* 3.9 23.1 - - + -
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Residues in contact with PHE 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 TRP* 3.2 64.5 + + - +
103A GLY* 3.9 4.5 - - - +
104A ARG 3.2 0.6 - - - -
105A PRO* 1.3 78.9 - - - +
107A TYR* 1.3 61.2 - - - +
109A LEU* 3.3 4.1 + - + +
110A ARG* 3.1 22.5 + - - +
150A LEU* 3.6 28.5 - - + -
168A ALA* 3.9 2.5 - - + -
169A PRO* 3.5 41.5 - - + -
171A ILE* 3.6 23.2 - - + +
506A EDO 3.6 32.8 - - - +
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Residues in contact with TYR 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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52A LEU* 3.7 33.7 - - + -
103A GLY 2.9 18.6 + - - +
104A ARG* 3.2 12.1 + - - +
106A PHE* 1.3 76.8 - - - +
108A ILE* 1.3 61.4 + - + +
110A ARG* 3.3 16.3 + - - +
111A GLU* 3.1 51.2 + - + +
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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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49A LEU* 3.9 14.8 - - + +
52A LEU* 3.6 22.0 - - + -
53A MSE 3.7 35.9 - - + +
58A TYR* 3.8 22.0 - - + -
104A ARG* 3.0 25.7 + - + +
105A PRO 3.8 3.6 - - - +
107A TYR* 1.3 78.2 - - - +
109A LEU* 1.3 52.0 + - - +
111A GLU* 3.2 5.9 + - - +
112A ALA* 2.8 33.3 + - + +
142A VAL* 3.6 21.8 - - + -
146A CYS* 3.6 17.3 - - - -
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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 PRO 3.0 21.2 + - - +
106A PHE* 3.5 7.2 - - + +
107A TYR 3.3 0.2 - - - -
108A ILE* 1.3 77.2 - - - +
110A ARG* 1.3 62.0 + - - +
112A ALA* 3.4 4.1 + - - +
113A TRP* 3.0 30.5 + - - +
143A ILE* 3.5 49.6 - - + +
146A CYS* 3.7 11.0 - - + -
147A GLN* 3.7 17.7 - - - +
150A LEU* 3.6 27.4 - - + -
171A ILE* 3.8 31.9 - - + +
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Residues in contact with ARG 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 PHE 3.1 12.6 + - - +
107A TYR* 3.5 21.3 - - - +
108A ILE 3.3 0.2 - - - -
109A LEU* 1.3 77.4 - - - +
111A GLU* 1.3 78.6 + - - +
113A TRP* 3.4 4.9 + - - +
114A ASN* 3.1 34.2 + - - +
171A ILE* 5.0 4.0 - - - +
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Residues in contact with GLU 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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49A LEU* 3.7 19.3 - - + -
52A LEU* 4.2 6.7 - - + -
107A TYR* 3.1 48.6 + - + +
108A ILE* 3.8 2.7 - - - +
110A ARG* 1.3 96.9 - - - +
112A ALA* 1.3 63.3 + - - +
114A ASN* 3.2 17.3 + - - +
115A ILE* 3.1 25.4 + - + +
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Residues in contact with ALA 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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49A LEU* 3.7 17.0 - - + +
108A ILE 2.8 21.7 + - - +
109A LEU* 3.7 2.9 - - - +
111A GLU* 1.3 74.5 - - - +
113A TRP* 1.3 61.8 + - - +
115A ILE* 3.1 7.1 + - - +
116A LEU* 3.1 18.7 + - - +
139A THR* 3.4 20.1 - - + +
142A VAL* 5.0 2.2 - - + -
143A ILE* 3.3 33.2 - - + +
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Residues in contact with TRP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.0 27.2 + - + +
110A ARG* 3.9 5.6 - - - +
111A GLU 3.3 0.2 - - - -
112A ALA* 1.3 74.3 - - - +
114A ASN* 1.3 61.4 + - - +
116A LEU* 3.8 29.0 - - + +
117A ASN* 2.9 32.4 + - + +
143A ILE* 3.8 21.5 - - + +
171A ILE* 2.9 34.7 + - + -
172A ASP* 3.3 31.6 - - - -
173A HIS* 3.6 18.6 - - - +
174A LEU* 3.8 27.5 - - + +
175A VAL 5.6 0.2 - - - +
192A PHE* 4.1 13.0 - + - -
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Residues in contact with ASN 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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36A PHE* 4.2 12.6 - - + -
110A ARG* 3.1 35.1 + - - +
111A GLU* 3.2 24.1 + - - +
113A TRP* 1.3 75.0 - - - +
115A ILE* 1.3 60.4 + - - +
117A ASN* 3.5 5.1 + - - +
118A ALA* 3.1 24.3 + - - +
174A LEU* 3.7 16.6 - - - +
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Residues in contact with ILE 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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36A PHE* 3.7 26.2 - - + -
42A VAL* 4.2 14.6 - - + -
45A ALA* 3.6 35.0 - - + +
46A VAL* 3.9 5.2 - - + +
49A LEU* 3.9 24.0 - - + -
111A GLU* 3.1 14.7 + - + +
112A ALA* 3.1 7.9 + - - +
114A ASN* 1.3 73.6 - - - +
116A LEU* 1.3 67.1 + - - +
118A ALA* 3.2 4.5 + - - +
119A ILE* 3.1 38.4 + - + +
139A THR* 3.7 19.1 - - + +
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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 ALA 3.1 15.6 + - - +
113A TRP* 3.3 34.3 + - + +
115A ILE* 1.3 75.6 - - - +
117A ASN* 1.3 57.5 + - - +
119A ILE* 3.2 8.1 + - + +
120A ALA* 2.8 31.9 + - - +
136A LYS* 3.9 37.2 - - + +
139A THR* 3.7 19.1 - - + -
140A MSE 4.0 15.9 - - + -
143A ILE* 3.5 24.2 - - + -
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Residues in contact with ASN 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 TRP* 2.9 19.5 + - + +
114A ASN* 3.9 4.5 - - - +
116A LEU* 1.3 73.8 - - - +
118A ALA* 1.3 60.7 + - - +
120A ALA* 3.3 8.0 + - - +
121A GLU* 2.9 61.3 + - - +
174A LEU* 3.6 39.1 - - + +
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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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36A PHE* 3.7 39.0 - - + -
114A ASN 3.1 14.9 + - - +
115A ILE 3.6 8.5 - - - +
117A ASN* 1.3 76.4 + - - +
119A ILE* 1.3 62.3 + - + +
121A GLU* 3.2 10.1 + - - -
123A LYS* 3.2 32.7 + - + +
124A ILE* 3.9 4.9 - - + -
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Residues in contact with ILE 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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42A VAL* 4.1 10.5 - - + -
115A ILE* 3.1 32.7 + - + +
116A LEU* 3.5 10.3 - - - +
118A ALA* 1.3 76.2 - - + +
120A ALA* 1.3 61.8 + - - +
122A GLY* 3.2 14.0 + - - -
124A ILE* 3.6 20.3 - - + +
132A LEU* 3.9 37.5 - - + +
136A LYS* 4.3 40.2 - - + +
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Residues in contact with ALA 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 2.8 20.4 + - - +
117A ASN* 3.8 11.4 - - - +
119A ILE* 1.3 75.0 - - - +
121A GLU* 1.3 61.0 + - + +
122A GLY 3.2 1.5 + - - -
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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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117A ASN* 2.9 47.3 + - - +
118A ALA* 3.9 6.4 - - - +
119A ILE 3.2 0.6 - - - -
120A ALA* 1.3 76.6 - - + +
122A GLY* 1.3 61.1 + - - +
123A LYS* 3.4 3.8 + - + +
174A LEU* 5.6 0.3 - - - +
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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