Contacts of the helix formed by residues 113 - 123 (chain N) in PDB entry 1MVW
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 LYS 113 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111N SER 5.4 1.3 - - - +
112N ILE* 1.3 75.8 - - + +
114N LYS* 1.3 65.5 + - - +
115N SER* 3.3 20.6 + - - +
116N PHE* 3.1 26.8 + - + +
117N LEU* 3.2 5.4 + - - +
146N GLY 2.9 3.8 - - - -
147N ASN* 3.0 12.0 - - - +
148N VAL* 4.4 6.3 - - - -
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Residues in contact with LYS 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N LYS* 1.3 66.7 - - - +
115N SER* 1.3 64.5 + - - +
118N GLU* 3.0 36.7 + - - +
137N TRP* 3.3 28.5 - - + +
146N GLY* 1.8 32.6 + - - +
147N ASN* 2.4 19.8 + - - -
148N VAL* 4.3 6.1 - - + +
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Residues in contact with SER 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N LYS* 3.3 22.6 + - - +
114N LYS* 1.3 79.4 - - - +
116N PHE* 1.3 59.0 + - - +
118N GLU* 3.2 14.8 + - - +
119N GLU* 3.0 49.0 + - - +
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Residues in contact with PHE 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LEU* 5.0 5.8 - - + -
112N ILE* 3.5 31.4 - - + -
113N LYS* 3.1 25.6 + - + +
115N SER* 1.3 79.6 + - - +
117N LEU* 1.3 60.2 + - + +
119N GLU* 3.3 12.8 + - - +
120N LEU* 2.9 60.0 + - + +
121O GLU* 5.0 12.6 - - - -
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Residues in contact with LEU 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N PHE* 5.2 11.2 - - + -
104N LEU* 4.2 19.5 - - + -
112N ILE* 3.5 32.5 - - + -
113N LYS 3.2 1.6 + - - +
114N LYS 3.3 0.2 + - - -
116N PHE* 1.3 81.6 - - + +
118N GLU* 1.3 55.0 + - - +
120N LEU* 4.5 7.0 - - + +
121N LEU* 3.0 34.1 + - - +
144N VAL 5.0 0.9 - - - +
147N ASN* 1.7 86.4 - - + +
150N TYR* 5.7 1.8 - - + -
153N ILE* 6.5 0.2 - - + -
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Residues in contact with GLU 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N LYS* 3.0 32.2 + - - +
115N SER* 3.2 22.9 + - - +
116N PHE 3.3 0.2 - - - -
117N LEU* 1.3 77.0 - - - +
119N GLU* 1.3 62.4 + - + +
122N THR* 3.0 30.9 + - - -
133N ILE* 3.5 33.2 - - + +
137N TRP* 3.1 24.4 + - - +
147N ASN* 4.1 4.0 - - - +
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Residues in contact with GLU 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N SER* 3.0 34.6 + - - +
116N PHE* 3.7 11.7 - - - +
118N GLU* 1.3 80.5 - - + +
120N LEU* 1.3 57.7 + - - +
122N THR* 3.8 1.9 - - - -
123N THR* 2.8 43.8 + - + +
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Residues in contact with LEU 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809M ARG* 4.8 25.4 - - - +
813M ILE* 5.9 3.5 - - + +
104N LEU* 3.7 31.4 - - + -
116N PHE* 2.9 40.9 + - + +
117N LEU* 4.2 6.3 - - + +
119N GLU* 1.3 74.6 - - - +
121N LEU* 1.3 65.4 + - - +
123N THR* 3.7 8.7 - - - +
124N GLY* 3.6 18.0 + - - +
125N GLY 4.7 0.2 + - - -
128N PHE* 4.5 2.3 - - - -
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Residues in contact with LEU 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N LEU 3.0 19.6 + - - +
118N GLU 3.9 2.2 - - - +
120N LEU* 1.3 74.7 - - - +
122N THR* 1.3 61.6 + - - +
125N GLY 2.9 12.5 + - - +
127N ARG 4.3 5.2 - - - +
128N PHE* 0.6 158.9 - - + +
132N GLU* 5.9 1.1 - - + -
133N ILE* 4.0 16.4 - - + -
136N MET* 5.2 14.1 - - + -
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Residues in contact with THR 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N GLU 3.0 15.9 + - - -
119N GLU* 3.8 3.4 - - - -
121N LEU* 1.3 77.6 - - - +
123N THR* 1.3 63.4 + - + +
124N GLY 3.0 3.6 + - - -
125N GLY 2.6 20.5 + - - +
128N PHE 2.9 19.3 + - - -
129N THR* 4.5 2.9 - - - -
130N PRO* 3.9 23.3 - - + +
133N ILE* 3.3 8.0 - - - +
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Residues in contact with THR 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119N GLU* 2.8 39.0 + - + +
120N LEU* 3.7 12.0 - - - +
122N THR* 1.3 76.7 - - + +
124N GLY* 1.2 58.3 + - - +
19O ARG* 4.3 24.3 + - - +
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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