Contacts of the helix formed by residues 102 - 121 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 4.2 4.5 - - + +
100B SER 3.2 0.6 - - - -
101B LEU* 1.3 77.6 - - - +
103B GLY* 1.3 73.0 + - - +
104B ARG 3.5 0.6 + - - -
105B PRO* 3.5 2.9 - - - +
106B PHE* 3.3 56.5 + + + -
150B LEU* 3.8 2.2 - - - +
154B PHE* 3.7 34.0 - + + -
168B ALA* 4.3 6.1 - - + -
169B PRO* 3.5 30.5 - - + -
460B ILE* 3.9 32.5 - - + -
461B PRO* 3.6 31.6 - - + -
464B GLN* 3.7 35.8 - - + +
471B MSE 5.6 0.7 - - - -
510B EDO 3.6 12.4 + - - +
515B EDO 3.7 14.9 + - - -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 1.3 82.5 - - - +
104B ARG* 1.3 55.7 + - - +
106B PHE* 3.6 3.4 + - - +
107B TYR* 2.9 30.3 + - - +
510B EDO 2.9 32.1 - - - -
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASP 4.8 0.2 + - - -
52B LEU* 2.8 67.6 + - - +
55B GLY* 4.2 14.1 - - - -
57B GLY* 5.1 0.7 - - - -
58B TYR* 3.8 20.4 - - + +
100B SER* 3.0 32.1 + - - +
103B GLY* 1.3 73.6 - - - +
105B PRO* 1.4 68.2 - - + +
107B TYR* 3.2 10.3 + - - +
108B ILE* 3.0 38.8 + - + +
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Residues in contact with PRO 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 3.9 31.4 - - + -
100B SER 3.2 13.5 - - - +
101B LEU* 3.3 22.9 - - + +
102B TRP 3.5 2.9 - - - +
104B ARG* 1.4 92.0 - - + +
106B PHE* 1.3 56.1 + - - +
108B ILE* 3.3 3.2 + - + +
109B LEU* 2.9 34.7 + - - +
146B CYS* 3.9 24.1 - - + +
149B ASP* 5.3 2.9 - - + -
150B LEU* 3.8 20.0 - - + -
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Residues in contact with PHE 106 (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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102B TRP* 3.3 63.6 + + - +
103B GLY* 3.9 4.3 - - - +
104B ARG 3.3 0.4 - - - -
105B PRO* 1.3 74.5 - - - +
107B TYR* 1.3 65.8 + - - +
109B LEU* 3.3 5.0 + - + +
110B ARG* 3.2 30.3 + - - +
150B LEU* 3.6 26.7 - - + +
168B ALA* 3.8 8.7 - - + -
169B PRO* 3.4 37.2 - - + -
171B ILE* 3.7 27.4 - - + -
515B EDO 3.7 29.2 - - - +
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.7 36.1 - - + -
103B GLY 2.9 19.1 + - - +
104B ARG* 3.2 14.6 + - - +
106B PHE* 1.3 78.0 - - - +
108B ILE* 1.3 64.8 + - - +
110B ARG* 3.3 8.8 + - + +
111B GLU* 3.1 55.6 + - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.0 14.3 - - + +
52B LEU* 3.7 24.0 - - + -
53B MSE 3.7 28.5 - - + +
58B TYR* 3.7 29.2 - - + -
104B ARG* 3.0 24.4 + - + +
105B PRO 3.6 3.8 - - - +
107B TYR* 1.3 75.0 - - - +
109B LEU* 1.3 60.6 + - - +
111B GLU* 3.2 7.4 + - - +
112B ALA* 2.8 28.1 + - + +
142B VAL* 3.6 22.4 - - + -
146B CYS* 3.5 17.7 - - - -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PRO 2.9 16.0 + - - +
106B PHE* 3.6 7.6 - - + +
108B ILE* 1.3 77.4 - - - +
110B ARG* 1.3 56.8 + - - +
112B ALA* 3.3 5.0 + - - +
113B TRP* 2.9 36.3 + - - -
143B ILE* 3.5 49.8 - - + +
146B CYS* 3.6 10.8 - - + -
147B GLN* 3.6 21.8 - - + +
150B LEU* 3.6 30.7 - - + -
171B ILE* 3.8 29.2 - - + +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.2 16.3 + - - +
107B TYR* 3.8 9.9 - - + +
109B LEU* 1.3 76.0 - - - +
111B GLU* 1.3 64.4 + - + +
113B TRP* 3.4 6.6 + - - +
114B ASN* 3.2 29.7 + - - +
171B ILE* 4.8 17.7 - - + +
174B LEU* 5.2 0.5 - - - +
175B VAL* 3.1 32.7 + - + +
176B GLY 3.0 23.2 + - - -
177B THR* 3.9 13.4 + - - +
179B GLU 3.2 24.5 + - - -
180B ASN* 5.1 1.2 - - - +
181B PRO* 4.3 0.2 - - - +
515B EDO 3.5 31.7 + - - -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.8 15.7 - - + -
52B LEU* 4.2 7.9 - - + +
107B TYR* 3.1 50.8 + - + +
108B ILE* 3.6 6.7 - - - +
110B ARG* 1.3 78.8 - - - +
112B ALA* 1.3 61.7 + - - +
114B ASN* 3.3 27.8 + - - +
115B ILE* 3.4 17.2 + - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.7 17.4 - - + +
108B ILE 2.8 21.2 + - - +
109B LEU* 3.7 0.9 - - - +
111B GLU* 1.3 72.0 - - - +
113B TRP* 1.3 63.9 + - - +
115B ILE* 3.1 4.1 + - - -
116B LEU* 3.0 18.4 + - - +
139B THR* 3.4 26.3 - - + +
142B VAL* 4.9 4.5 - - + -
143B ILE* 3.4 29.4 - - + -
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 2.9 26.8 + - - +
110B ARG* 3.9 6.3 - - - +
111B GLU 3.3 0.2 - - - -
112B ALA* 1.3 75.8 - - - +
114B ASN* 1.3 58.3 + - - +
116B LEU* 3.2 33.0 + - + +
117B ASN* 2.8 34.0 + - + +
143B ILE* 4.0 19.8 - - + +
171B ILE* 2.9 36.0 + - + -
172B ASP* 3.4 29.4 - - - -
173B HIS* 3.5 28.0 - - - +
174B LEU* 3.8 18.2 - - + +
175B VAL 5.3 0.9 - - - +
192B PHE* 4.1 13.0 - + - -
196B THR* 6.4 0.7 - - + -
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Residues in contact with ASN 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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36B PHE* 4.7 14.3 - - + -
110B ARG* 3.2 17.5 + - - +
111B GLU* 3.5 25.6 + - - +
112B ALA 3.3 0.2 - - - -
113B TRP* 1.3 75.3 - - - +
115B ILE* 1.3 61.9 + - - +
117B ASN* 3.9 1.8 - - - +
118B ALA* 3.1 25.1 + - - +
174B LEU* 3.3 21.4 - - - +
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Residues in contact with ILE 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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36B PHE* 3.5 28.0 - - + -
42B VAL* 3.9 27.6 - - + -
45B ALA* 3.6 34.3 - - + +
46B VAL* 3.9 4.7 - - + +
49B LEU* 4.0 23.1 - - + -
111B GLU* 3.4 14.6 + - + +
112B ALA* 3.1 7.7 + - - +
114B ASN* 1.3 78.7 - - - +
116B LEU* 1.3 63.6 + - - +
117B ASN 3.3 0.2 + - - -
118B ALA* 3.3 2.1 + - - +
119B ILE* 3.1 28.5 + - + +
139B THR* 3.9 14.8 - - + +
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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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112B ALA 3.0 14.8 + - - +
113B TRP* 3.2 35.2 + - + +
115B ILE* 1.3 75.8 - - - +
117B ASN* 1.3 57.3 + - - +
119B ILE* 3.3 7.6 + - + +
120B ALA* 2.8 31.0 + - - +
136B LYS* 3.8 45.1 - - + +
139B THR* 4.0 13.5 - - + -
140B MSE 3.9 16.2 - - + -
143B ILE* 3.4 26.2 - - + -
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Residues in contact with ASN 117 (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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113B TRP* 2.8 23.2 + - + +
114B ASN* 3.9 3.8 - - - +
116B LEU* 1.3 71.0 - - - +
118B ALA* 1.3 59.5 + - - +
120B ALA* 3.4 7.5 + - - +
121B GLU* 2.9 68.0 + - - +
174B LEU* 3.7 39.4 - - + +
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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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36B PHE* 4.5 28.0 - - + -
114B ASN 3.1 18.6 + - - +
115B ILE 3.3 5.1 + - - +
117B ASN* 1.3 77.3 + - - +
119B ILE* 1.3 62.0 + - - +
121B GLU* 3.4 6.2 + - - -
123B LYS* 3.1 47.7 + - + +
124B ILE* 4.3 6.0 + - + -
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.1 16.8 - - + -
115B ILE* 3.1 24.8 + - + +
116B LEU* 3.6 9.0 - - + +
118B ALA* 1.3 77.2 - - + +
120B ALA* 1.3 61.4 + - - +
122B GLY* 3.1 15.1 + - - -
124B ILE* 4.2 14.1 + - + -
132B LEU* 3.9 41.7 - - + -
136B LYS* 4.1 43.3 - - + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU 2.8 20.4 + - - +
117B ASN* 3.4 12.1 + - - +
119B ILE* 1.3 73.9 - - - +
121B GLU* 1.3 61.3 + - + +
122B GLY 3.2 1.1 + - - -
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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
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117B ASN* 2.9 47.0 + - - +
118B ALA* 3.4 5.2 + - - +
119B ILE 3.2 0.4 - - - -
120B ALA* 1.3 76.0 - - + +
122B GLY* 1.3 62.5 + - - +
123B LYS* 2.6 46.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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