Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 4IBR
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 ASP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LYS* 4.0 0.9 + - - -
104A TYR* 4.1 6.1 - - - -
105A SER* 3.2 8.9 - - - -
106A PRO* 3.5 3.0 - - + -
107A VAL* 2.9 31.5 + - + -
108A THR* 2.8 36.2 + - - -
124A ALA* 3.0 22.0 + - + +
125A ALA* 3.8 3.9 - - - +
128A MET* 3.1 5.1 - - + -
129A SER* 1.3 74.3 - - - +
131A ASN* 1.3 63.4 + - - +
132A THR 3.3 3.5 + - - -
133A ALA* 2.9 29.7 + - + +
134A ALA* 3.3 20.3 + - - +
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Residues in contact with ASN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 4.6 0.3 + - - -
72A LYS* 3.1 14.8 + - - +
102A VAL* 3.5 13.2 - - + -
103A LYS* 2.8 24.8 + - - +
104A TYR* 3.1 29.2 + - - +
129A SER 3.8 1.7 - - - +
130A ASP* 1.3 68.3 + - - +
132A THR* 1.3 65.8 + - - +
134A ALA* 3.1 6.3 + - - +
135A ASN* 3.0 24.3 + - - +
165A GLU* 2.8 41.2 + - + +
166A PRO* 4.7 8.3 - - - +
169A ASN* 4.9 2.3 + - - +
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Residues in contact with THR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.8 4.5 - - + -
100A ASP* 3.7 18.2 - - + +
101A LEU* 3.4 9.2 - - + -
102A VAL* 3.0 24.9 + - - +
105A SER* 2.8 18.6 + - - -
108A THR* 3.3 22.0 - - - +
130A ASP* 3.3 1.4 + - - -
131A ASN* 1.3 74.2 - - - +
133A ALA* 1.3 68.0 + - - +
135A ASN* 3.1 7.4 + - + +
136A LEU* 2.8 44.0 + - + +
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Residues in contact with ALA 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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108A THR* 3.6 12.9 - - + +
121A LEU* 3.4 33.6 - - + +
124A ALA* 4.0 4.0 - - + -
125A ALA 3.9 3.1 - - - +
130A ASP* 2.9 34.2 + - + +
132A THR* 1.3 77.3 - - - +
134A ALA* 1.3 56.2 + - - +
136A LEU* 3.2 2.6 + - - +
137A LEU* 2.9 35.5 + - - +
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Residues in contact with ALA 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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71A PHE* 4.3 9.0 - - + -
72A LYS* 3.8 39.0 - - + -
75A LEU* 3.4 16.3 - - + +
125A ALA* 4.1 5.5 - - + +
130A ASP 3.3 3.0 + - - +
131A ASN 3.1 9.1 + - - +
133A ALA* 1.3 80.3 - - - +
135A ASN* 1.3 57.8 + - - +
137A LEU* 3.3 0.7 + - - -
138A LEU* 2.9 33.1 + - - +
165A GLU* 4.5 3.4 - - + -
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Residues in contact with ASN 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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100A ASP 5.3 2.7 + - - +
102A VAL* 3.8 22.8 - - - +
131A ASN 3.0 12.4 + - - +
132A THR* 3.1 10.7 + - + +
134A ALA* 1.3 73.0 - - - +
136A LEU* 1.3 67.4 + - + +
138A LEU* 3.3 3.7 + - - +
139A THR* 3.0 20.1 + - - -
164A TRP* 3.3 35.4 - - + +
165A GLU* 3.1 47.2 + - - +
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Residues in contact with LEU 136 (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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94A ILE* 4.5 13.6 - - + +
95A HIS 5.4 0.4 - - - +
96A TYR* 3.6 45.5 - - + -
100A ASP* 5.1 7.4 - - + -
108A THR* 4.4 0.9 - - + -
121A LEU* 3.6 35.0 - - + -
132A THR* 2.8 35.6 + - + +
133A ALA* 3.5 5.6 - - - +
135A ASN* 1.3 72.0 - - + +
137A LEU* 1.3 62.0 + - - +
139A THR* 3.2 11.6 + - - +
140A THR* 3.2 25.2 + - - +
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Residues in contact with LEU 137 (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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75A LEU* 3.8 18.4 - - + -
76A CYS* 3.9 7.0 - - - -
79A VAL* 4.1 8.5 - - + -
118A VAL* 3.8 35.7 - - + +
121A LEU* 3.6 35.7 - - + +
122A CYS* 3.8 22.7 - - - +
125A ALA* 4.1 9.6 - - + -
133A ALA 2.9 20.3 + - - +
134A ALA 3.7 4.0 - - - +
135A ASN 3.3 0.2 - - - -
136A LEU* 1.3 73.2 - - - +
138A LEU* 1.3 65.8 + - - +
140A THR* 2.5 29.4 + - + +
141A ILE* 3.3 8.5 + - - +
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Residues in contact with LEU 138 (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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71A PHE* 4.4 9.9 - - + -
75A LEU* 3.7 22.4 - - + -
134A ALA 2.9 18.6 + - - +
135A ASN* 3.3 14.8 + - - +
137A LEU* 1.3 76.5 - - - +
139A THR* 1.3 56.9 + - - +
141A ILE* 3.2 9.5 + - + +
142A GLY 3.0 5.5 + - - -
143A GLY* 2.7 34.9 + - - +
144A PRO* 3.8 27.1 - - + -
147A LEU* 4.7 4.0 - - + -
161A LEU* 4.1 22.4 - - + -
164A TRP* 3.6 36.3 - - + -
165A GLU 5.4 0.2 - - - +
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Residues in contact with THR 139 (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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135A ASN 3.0 13.4 + - - -
136A LEU* 3.4 14.6 - - - +
138A LEU* 1.3 77.0 - - - +
140A THR* 1.3 65.6 + - + +
141A ILE 3.1 1.0 + - - -
142A GLY* 3.2 11.2 + - - +
143A GLY 4.6 1.1 - - - +
164A TRP* 3.8 16.6 - - - -
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Residues in contact with THR 140 (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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79A VAL* 4.3 6.8 - - - +
82A ARG* 3.5 21.2 + - - -
88A GLU* 3.8 18.0 + - - +
92A ARG* 3.9 12.8 + - - +
94A ILE* 3.5 29.4 - - + -
118A VAL* 5.0 3.7 - - + +
136A LEU 3.2 14.6 - - - +
137A LEU* 2.5 26.5 + - + +
139A THR* 1.3 80.0 - - + +
141A ILE* 1.3 67.5 + - - +
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Residues in contact with ILE 141 (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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75A LEU* 3.6 22.2 - - + -
78A ALA* 4.4 12.6 - - + -
79A VAL* 3.9 21.5 - - + +
82A ARG* 3.7 29.0 + - - +
137A LEU 3.8 5.4 - - - +
138A LEU* 3.2 15.0 + - + +
140A THR* 1.3 89.5 + - - +
142A GLY* 1.3 57.0 + - - +
143A GLY 4.1 7.4 - - - +
146A GLU* 3.6 19.0 - - + +
147A LEU* 4.1 31.0 - - + +
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Residues in contact with GLY 142 (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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138A LEU 3.0 2.2 + - - -
139A THR* 3.2 9.5 + - - -
141A ILE* 1.3 80.3 - - - +
143A GLY* 1.3 62.3 + - - +
145A LYS* 5.1 1.7 + - - +
146A GLU* 3.4 19.2 + - - +
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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