Contacts of the helix formed by residues 119 - 128 (chain L) 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 THR 119 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117L LYS 4.0 2.8 + - - +
118L MET* 1.3 73.4 - - - +
120L GLU* 1.3 59.8 + - - +
121L GLU* 3.4 12.1 + - - +
122L GLU* 2.9 41.0 + - - +
123L VAL* 3.0 25.6 + - - +
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Residues in contact with GLU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ARG* 3.7 32.1 + - - +
109L HIS* 5.1 6.8 - - - -
112L ALA* 3.7 22.8 - - + +
118L MET 3.6 0.8 + - - -
119L THR* 1.3 73.7 - - - +
121L GLU* 1.3 56.1 + - - +
123L VAL* 3.7 12.7 - - - +
124L GLU* 3.0 60.3 + - - +
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Residues in contact with GLU 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809J ARG* 5.6 3.6 + - - -
116K PHE* 4.6 17.7 - - - -
119L THR* 3.4 10.1 + - - +
120L GLU* 1.3 76.4 - - - +
122L GLU* 1.3 62.4 + - + +
124L GLU* 3.2 12.7 + - - +
125L GLU* 3.0 48.3 + - - +
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Residues in contact with GLU 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798J LEU* 3.9 30.8 - - + +
799J MET* 5.4 6.9 - - - +
802J GLU* 5.1 13.9 - - + +
118L MET* 4.0 6.7 - - - +
119L THR* 2.9 45.9 + - - +
121L GLU* 1.3 76.1 - - + +
123L VAL* 1.3 62.6 + - - +
125L GLU* 3.1 17.8 + - - +
126L LEU* 3.0 30.6 + - - +
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Residues in contact with VAL 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ARG* 3.6 38.6 - - + +
111L LEU* 3.8 39.9 - - + -
112L ALA 4.3 0.9 - - - +
118L MET* 3.9 11.7 - - + +
119L THR 3.0 18.6 + - - +
120L GLU* 3.6 23.6 - - - +
121L GLU 3.3 0.2 - - - -
122L GLU* 1.3 74.0 - - - +
124L GLU* 1.3 63.7 + - - +
126L LEU* 3.1 9.9 + - - +
127L MET* 3.0 26.2 - - + +
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Residues in contact with GLU 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ARG* 5.3 7.2 - - - +
120L GLU* 3.0 50.1 + - - +
121L GLU* 3.2 8.7 + - - +
123L VAL* 1.3 73.7 - - - +
125L GLU* 1.3 59.1 + - + +
127L MET* 3.2 6.0 + - - +
128L LYS* 3.0 32.5 + - - +
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Residues in contact with GLU 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801J VAL* 4.0 20.8 - - + +
802J GLU* 3.6 23.9 - - - +
805J ALA* 6.3 0.7 - - - -
809J ARG* 5.3 5.9 + - - -
121L GLU* 3.0 37.4 + - + +
122L GLU* 3.1 28.1 + - - +
124L GLU* 1.3 78.3 - - + +
126L LEU* 1.3 60.8 + - + +
128L LYS* 4.1 35.4 - - - +
130L GLN* 5.3 0.2 - - - +
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Residues in contact with LEU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797J PHE* 2.7 23.8 - - + -
798J LEU* 2.0 54.5 - - + +
801J VAL* 2.7 45.3 - - + -
111L LEU* 4.2 13.0 - - + -
122L GLU 3.0 15.3 + - - +
123L VAL* 3.1 5.3 + - - +
125L GLU* 1.3 79.2 - - + +
127L MET* 1.3 64.7 + - - +
128L LYS 3.5 0.2 - - - -
130L GLN* 3.1 24.7 + - - +
142L PHE* 3.2 13.2 - - + -
146L ILE* 4.1 1.1 - - + +
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Residues in contact with MET 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L LEU* 3.9 24.0 - - + -
108L ARG* 4.4 13.5 - - + -
111L LEU* 5.3 1.3 - - - -
123L VAL* 3.0 29.5 + - + +
124L GLU* 3.2 4.9 + - - +
126L LEU* 1.3 87.2 - - - +
128L LYS* 1.3 56.9 + - - +
129L GLY 3.0 9.5 + - - -
130L GLN* 3.0 12.4 - - - +
131L GLU* 3.1 33.2 + - - +
137L ILE* 3.5 48.5 - - + -
142L PHE* 3.8 19.3 - - + -
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Residues in contact with LYS 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805J ALA* 6.3 0.6 - - - +
106K PRO* 6.5 0.9 - - + -
124L GLU 3.0 17.0 + - - +
125L GLU* 4.1 34.4 - - - +
126L LEU 3.5 0.6 - - - -
127L MET* 1.3 73.0 - - - +
129L GLY* 1.3 59.0 + - - +
130L GLN* 3.4 8.1 + - - +
131L GLU 5.8 0.2 - - - -
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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