Contacts of the helix formed by residues 113 - 123 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111H SER 3.9 1.3 + - - +
112H ILE* 1.3 75.2 - - + +
114H LYS* 1.3 65.1 + - - +
115H SER* 3.3 20.6 + - - +
116H PHE* 3.1 27.0 + - + +
117H LEU* 3.2 4.7 + - - +
146H GLY 2.9 3.6 - - - -
147H ASN* 3.0 11.4 - - - +
148H VAL* 4.4 6.5 - - + -
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Residues in contact with LYS 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H LYS* 1.3 67.1 - - - +
115H SER* 1.3 63.2 + - - +
118H GLU* 3.0 36.6 + - - +
137H TRP* 3.3 29.4 - - + +
146H GLY* 1.8 30.9 + - - +
147H ASN* 2.4 19.9 + - - -
148H VAL* 4.3 6.8 - - + +
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Residues in contact with SER 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H LYS* 3.3 22.3 + - - +
114H LYS* 1.3 79.5 - - - +
116H PHE* 1.3 60.4 + - - +
118H GLU* 3.2 15.4 + - - +
119H GLU* 3.0 49.4 + - - +
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Residues in contact with PHE 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809G ARG* 5.8 4.7 - - - -
104H LEU* 5.0 5.2 - - + -
112H ILE* 3.5 31.2 - - + -
113H LYS* 3.1 25.4 + - + +
115H SER* 1.3 80.5 + - - +
117H LEU* 1.3 59.4 + - + +
119H GLU* 3.7 12.2 - - - +
120H LEU* 2.9 59.1 + - + +
121I GLU* 4.9 15.0 - - - -
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Residues in contact with LEU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H PHE* 5.2 11.7 - - + -
104H LEU* 4.2 19.7 - - + -
112H ILE* 3.5 32.3 - - + -
113H LYS 3.2 1.6 + - - +
114H LYS 3.3 0.2 + - - -
116H PHE* 1.3 81.7 - - + +
118H GLU* 1.3 55.8 + - - +
120H LEU* 4.5 5.8 - - + +
121H LEU* 3.0 33.9 + - - +
144H VAL 5.0 0.7 - - - +
147H ASN* 1.7 88.2 - - + +
150H TYR* 5.7 1.3 - - + -
153H ILE* 6.5 0.2 - - + -
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Residues in contact with GLU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H LYS* 3.0 32.4 + - - +
115H SER* 3.2 22.7 + - - +
116H PHE 3.3 0.2 - - - -
117H LEU* 1.3 78.1 - - - +
119H GLU* 1.3 63.0 + - + +
122H THR* 3.0 30.5 + - - -
133H ILE* 3.5 33.7 - - + +
137H TRP* 3.1 24.5 + - - +
147H ASN* 4.1 4.0 - - - +
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Residues in contact with GLU 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H SER* 3.0 32.6 + - - +
116H PHE* 3.7 12.1 - - - +
118H GLU* 1.3 80.5 - - + +
120H LEU* 1.3 57.8 + - - +
122H THR* 3.8 2.4 - - - -
123H THR* 2.8 43.8 + - + +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809G ARG* 4.3 33.2 - - - +
813G ILE* 5.3 9.5 - - + +
104H LEU* 3.7 31.0 - - + -
116H PHE* 2.9 40.9 + - + +
117H LEU* 4.2 7.0 - - + +
119H GLU* 1.3 74.4 - - - +
121H LEU* 1.3 65.3 + - - +
123H THR* 3.7 9.2 - - - +
124H GLY* 3.6 18.1 + - - +
128H PHE* 4.5 2.1 - - - -
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Residues in contact with LEU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817G GLN* 5.0 0.2 - - + -
117H LEU 3.0 18.9 + - - +
118H GLU 3.9 2.5 - - - +
120H LEU* 1.3 75.1 - - - +
122H THR* 1.3 59.1 + - - +
125H GLY 2.9 13.0 + - - +
127H ARG 4.3 4.3 - - - +
128H PHE* 0.6 160.7 - - + +
132H GLU* 5.9 1.3 - - + -
133H ILE* 4.0 16.6 - - + -
136H MET* 5.2 14.6 - - + -
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Residues in contact with THR 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H GLU 3.0 16.2 + - - -
119H GLU* 3.8 3.4 - - - -
121H LEU* 1.3 78.4 - - - +
123H THR* 1.3 62.4 + - + +
124H GLY 3.0 4.1 + - - -
125H GLY 2.6 20.4 + - - +
128H PHE 2.9 19.6 + - - -
129H THR* 4.5 3.1 - - - -
130H PRO* 3.9 22.9 - - + +
133H ILE* 3.3 8.1 - - - +
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Residues in contact with THR 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806G MET* 6.1 1.2 - - - +
119H GLU* 2.8 38.7 + - + +
120H LEU* 3.7 11.8 + - - +
122H THR* 1.3 76.9 - - + +
124H GLY* 1.2 58.1 + - - +
19I ARG* 5.7 3.3 + - - -
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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