Contacts of the helix formed by residues 127 - 135 (chain A) in PDB entry 3IMJ
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 SER 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.7 11.7 - - - -
125A PHE* 3.2 10.0 + - - +
126A ASN* 1.3 81.4 - - - +
128A LEU* 1.3 62.4 + - - +
129A ASN* 3.6 2.9 + - - +
130A GLU* 2.6 38.2 + - - +
131A LEU* 3.2 18.4 + - - +
64B LYS* 3.7 16.5 - - - +
87B GLU* 3.5 25.8 - - - -
93B GLY* 5.5 0.2 - - - -
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Residues in contact with LEU 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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60A TRP* 4.2 11.0 - - + -
61A PHE* 4.5 1.3 - - + -
85A ILE* 4.3 19.5 - - + -
95A PHE* 4.0 33.0 - - + -
110A VAL* 3.9 30.7 - - + -
118A TYR* 3.8 18.9 - - + -
127A SER* 1.3 70.4 - - - +
129A ASN* 1.3 56.6 + - - +
131A LEU* 3.2 8.8 + - + +
132A VAL* 2.9 35.0 + - + +
61B PHE* 4.2 13.9 - - + -
87B GLU* 2.9 15.7 + - - +
95B PHE* 3.9 23.6 - - + -
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Residues in contact with ASN 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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58A HIS* 2.9 32.5 + - - -
60A TRP* 3.8 14.9 - - + -
127A SER* 3.2 5.8 - - - +
128A LEU* 1.3 77.7 - - - +
130A GLU* 1.3 55.8 + - + +
132A VAL* 3.6 0.9 + - - +
133A ASP* 3.0 46.9 + - - +
62B PHE 4.2 0.3 - - - +
63B GLY* 4.1 2.2 - - - -
64B LYS* 2.9 33.0 + - + +
87B GLU* 2.9 16.9 + - - +
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Residues in contact with GLU 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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125A PHE* 3.8 15.8 - - + -
126A ASN* 3.4 15.6 + - - +
127A SER* 2.6 34.4 + - - +
129A ASN* 1.3 75.0 - - + +
131A LEU* 1.3 60.4 + - - +
133A ASP* 4.1 5.6 - - - +
134A TYR* 3.1 30.8 + - - +
64B LYS* 3.0 34.3 + - + +
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Residues in contact with LEU 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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85A ILE* 4.9 6.3 - - + -
97A LEU* 5.1 5.8 - - + -
110A VAL* 4.1 18.2 - - + -
118A TYR* 3.9 11.2 - - + -
119A PHE* 3.8 34.8 - - - +
120A LEU* 4.2 21.5 - - + -
125A PHE* 3.8 30.0 - - + -
127A SER 3.2 12.2 + - - +
128A LEU* 3.2 12.9 + - + +
130A GLU* 1.3 74.9 - - - +
132A VAL* 1.3 73.2 + - + +
134A TYR* 3.6 0.7 + - - +
135A HIS* 3.1 38.6 + - + -
148A LEU* 5.9 0.7 - - + -
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Residues in contact with VAL 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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60A TRP* 3.7 28.0 - - + +
83A PHE* 3.5 35.0 - - + -
85A ILE* 3.9 32.8 - - + -
128A LEU 2.9 19.6 + - - +
129A ASN 3.8 3.4 - - - +
131A LEU* 1.3 81.3 - - + +
133A ASP* 1.3 66.4 + - - +
135A HIS* 3.1 13.9 + - - +
136A ARG* 3.4 21.7 + - - +
148A LEU* 3.8 9.5 - - + +
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Residues in contact with ASP 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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58A HIS* 5.8 0.9 - - - -
60A TRP* 5.1 0.5 + - - -
129A ASN* 3.0 40.3 + - - +
130A GLU* 4.1 5.6 - - - +
132A VAL* 1.3 72.3 - - - +
134A TYR* 1.3 64.8 + - - +
136A ARG* 3.1 46.4 + - - +
137A SER* 4.3 1.7 + - - -
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Residues in contact with TYR 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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123A VAL* 4.0 28.2 - - + +
125A PHE* 3.4 33.2 - + + -
130A GLU 3.1 20.1 + - - +
131A LEU 3.8 1.8 - - - +
133A ASP* 1.3 74.7 - - - +
135A HIS* 1.3 78.3 + + - +
136A ARG 3.1 5.4 + - - -
137A SER* 3.2 14.0 + - - -
138A THR* 3.3 45.2 + - + +
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Residues in contact with HIS 135 (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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120A LEU* 3.8 25.9 - - + +
121A TRP* 4.6 10.4 - + - -
125A PHE* 4.3 9.6 - + - -
131A LEU* 3.1 32.4 + - + +
132A VAL 3.1 8.5 + - - +
134A TYR* 1.3 101.5 - + - +
136A ARG* 1.3 57.2 + - - +
137A SER 3.2 1.8 - - - -
138A THR* 3.1 27.6 + - + +
139A SER 3.5 17.7 + - - -
140A VAL* 3.6 26.1 - - + +
147A PHE* 3.9 2.6 - - - -
148A LEU* 3.1 28.9 + - + +
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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