Contacts of the helix formed by residues 104 - 114 (chain C) 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 GLY 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C VAL 3.4 1.4 + - - -
103C MET* 1.3 71.8 - - - +
105C ALA* 1.3 61.3 + - - +
106C GLU 3.1 0.5 + - - -
107C LEU* 3.1 13.3 + - - +
108C ARG* 3.2 25.2 + - - +
131C GLU* 3.1 25.8 - - - -
135C GLY* 2.9 13.5 + - - -
137C ILE* 3.6 10.4 - - - +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C MET* 3.4 1.4 - - - +
104C GLY* 1.3 72.3 - - - +
106C GLU* 1.3 62.9 + - + +
108C ARG* 3.7 26.4 - - - +
109C HIS* 3.0 52.6 + - + +
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 3.8 33.4 - - + +
95C ASP* 5.1 4.0 - - - +
96C LYS* 5.8 1.4 + - - -
102C VAL* 3.8 5.6 - - + +
103C MET* 2.9 56.6 + - + +
105C ALA* 1.3 75.6 - - + +
107C LEU* 1.3 59.0 + - - +
109C HIS* 4.0 2.4 - - - +
110C VAL* 3.0 34.5 + - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 4.7 14.1 - - + -
94C PHE* 4.4 4.7 - - + -
102C VAL* 3.6 30.3 - - + -
103C MET 3.6 0.6 + - - -
104C GLY 3.1 2.0 + - - -
106C GLU* 1.3 78.4 - - - +
108C ARG* 1.3 60.0 + - - +
110C VAL* 3.4 4.1 + - + +
111C LEU* 2.9 45.6 + - + +
127C MET* 3.9 22.2 - - + -
137C ILE* 3.8 27.1 - - + -
142C PHE* 3.9 30.5 - - + -
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLY* 3.2 14.0 + - - +
105C ALA* 3.7 33.0 - - - +
106C GLU 3.3 0.2 - - - -
107C LEU* 1.3 78.5 - - + +
109C HIS* 1.3 70.8 + - + +
111C LEU* 3.4 2.1 + - - +
112C ALA* 3.1 24.4 + - - +
120C GLU* 3.7 25.2 + - - +
123C VAL* 3.6 20.7 - - + +
124C GLU* 5.3 7.6 - - - +
127C MET* 4.4 16.6 - - + -
131C GLU* 3.5 25.0 + - - +
137C ILE* 5.6 0.4 - - + -
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Residues in contact with HIS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA* 3.0 38.4 + - + +
106C GLU* 4.2 2.4 - - - +
108C ARG* 1.3 83.5 + - + +
110C VAL* 1.3 59.1 - - + +
112C ALA* 3.3 3.5 + - + -
113C THR* 2.8 43.6 + - + +
120C GLU* 5.0 7.2 - - - -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A ILE* 6.2 1.1 - - + -
94C PHE* 3.7 27.8 - - + -
106C GLU* 3.0 19.9 + - - +
107C LEU* 3.9 4.7 - - + +
109C HIS* 1.3 77.9 - - + +
111C LEU* 1.3 58.7 + - - +
114C LEU* 2.9 66.7 + - + +
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A GLN* 6.1 3.6 - - + -
794A CYS* 4.3 26.0 - - + -
107C LEU* 2.9 33.1 + - + +
108C ARG 3.9 2.7 - - - +
110C VAL* 1.3 77.5 - - - +
112C ALA* 1.3 59.0 + - - +
114C LEU 4.8 2.0 + - - +
116C GLU 4.0 4.5 - - - +
118C MET* 3.2 44.3 + - + +
123C VAL* 3.8 28.5 - - + -
126C LEU* 4.2 25.8 - - + -
127C MET* 5.3 1.6 - - - -
142C PHE* 5.9 2.2 - - + -
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Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG 3.1 16.8 + - - +
109C HIS* 4.0 3.4 - - + +
111C LEU* 1.3 80.5 - - - +
113C THR* 1.3 67.0 + - + +
114C LEU 3.8 0.2 - - - -
117C LYS* 3.3 29.7 - - - +
118C MET 3.1 20.3 + - - +
120C GLU* 3.7 19.5 - - + +
123C VAL* 4.4 1.6 - - + -
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Residues in contact with THR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C HIS* 2.8 28.0 + - + +
112C ALA* 1.3 87.3 - - + +
114C LEU* 1.3 76.6 + - - +
115C GLY 3.7 2.4 + - - -
117C LYS* 3.2 28.7 + - - +
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Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A ILE* 3.9 22.8 - - + +
791A GLN* 2.5 23.7 + - - +
110C VAL* 2.9 51.8 + - + +
111C LEU* 4.8 1.3 - - - +
112C ALA 3.8 0.8 - - - -
113C THR* 1.3 92.9 - - - +
115C GLY* 1.3 54.6 + - - +
116C GLU 4.5 2.4 - - - +
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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