Contacts of the helix formed by residues 127 - 134 (chain A) in PDB entry 4MT7
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 ILE 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ILE* 4.0 17.0 - - + -
58A ILE* 4.3 24.5 - - + -
59A MET* 6.2 2.0 - - - -
113A LEU* 4.0 22.0 - - + +
116A GLN* 4.7 7.2 - - + +
117A TYR* 6.0 0.4 - - - -
125A SER* 3.9 24.5 - - - +
126A GLU* 1.3 76.7 - - - +
128A GLY* 1.3 68.9 + - - +
129A PRO* 3.3 2.5 - - - -
130A CYS* 3.1 23.0 + - - +
131A PHE* 3.6 22.4 + - + -
200A LEU* 5.4 1.8 - - + -
203A LEU* 3.8 30.7 - - + -
213A ASP* 3.1 5.3 + - - +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 1.3 79.8 - - - +
129A PRO* 1.3 68.6 - - - +
130A CYS 3.1 0.9 + - - -
131A PHE* 3.1 8.4 + - - +
132A LEU* 3.0 24.4 + - - +
200A LEU* 6.3 1.3 - - - -
213A ASP* 3.3 6.6 + - - -
216A TYR* 3.8 26.5 - - - -
217A VAL* 4.0 7.3 - - - +
220A ALA* 4.1 4.9 - - - +
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Residues in contact with PRO 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLN* 4.8 8.3 - - - +
126A GLU* 3.7 24.0 - - + +
127A ILE 3.5 2.5 - - - -
128A GLY* 1.3 88.5 - - - +
130A CYS* 1.3 56.1 + - - +
132A LEU* 3.1 11.4 + - + +
133A GLU* 2.9 38.3 + - - +
213A ASP* 3.6 5.6 - - - +
216A TYR* 3.5 35.4 - - + -
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Residues in contact with CYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 4.0 11.0 - - + -
112A ASP* 3.7 24.5 - - + -
113A LEU* 3.6 28.5 - - + -
116A GLN* 3.5 31.2 - - - -
127A ILE 3.1 11.8 + - - +
128A GLY 3.1 0.6 + - - -
129A PRO* 1.3 76.7 - - - +
131A PHE* 1.3 67.6 + - + +
132A LEU 3.2 0.2 + - - -
133A GLU* 3.3 12.9 + - - +
134A HIS* 3.2 25.3 + - - +
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 5.5 9.9 - - + -
62A GLU* 6.3 0.7 - - + -
109A PHE* 3.7 31.9 - + - -
113A LEU* 5.1 7.0 - - + -
127A ILE* 3.8 28.0 - - + -
128A GLY* 3.1 8.8 + - - +
130A CYS* 1.3 79.6 - - + +
132A LEU* 1.3 58.5 + - - +
134A HIS 3.5 1.2 + - - -
135A GLN* 3.0 30.1 + - - +
138A PHE* 4.2 6.7 - + - -
196A TYR* 4.0 39.7 - + + -
199A GLN* 6.5 0.7 - - + -
200A LEU* 4.3 26.7 - - + -
220A ALA* 3.8 16.8 - - + -
223A VAL* 5.2 1.5 - - + +
224A MET* 3.8 30.0 - - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY 3.0 16.3 + - - +
129A PRO* 3.6 9.6 - - + +
130A CYS 3.1 0.2 - - - -
131A PHE* 1.3 77.3 - - - +
133A GLU* 1.3 61.5 + - - +
135A GLN* 2.8 43.1 + - - +
216A TYR* 3.9 36.1 - - + +
219A ALA* 4.1 13.2 - - + -
220A ALA* 3.7 28.3 - - + +
223A VAL* 3.8 14.1 - - + -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP* 3.7 23.8 - - - +
129A PRO* 2.9 24.1 + - - +
130A CYS* 3.6 13.8 - - - +
132A LEU* 1.3 76.3 - - - +
134A HIS* 1.3 73.9 + - + +
135A GLN* 3.3 2.3 + - - +
136A ASP* 5.0 4.3 + - - +
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Residues in contact with HIS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 4.0 16.8 - + + -
108A GLY 3.8 4.4 + - - -
109A PHE* 3.2 53.5 + + + -
112A ASP* 3.1 29.9 + - + +
130A CYS 3.2 12.2 + - - +
131A PHE 3.6 2.0 - - - -
133A GLU* 1.3 95.6 + - + +
135A GLN* 1.3 63.5 + - - +
136A ASP 3.1 3.1 - - - -
137A GLY* 3.0 17.1 + - - +
138A PHE* 3.0 16.1 - - + -
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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