Contacts of the strand formed by residues 142 - 153 (chain A) in PDB entry 5IXM
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 TRP 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A TYR* 3.7 28.7 - + + -
138A ALA* 3.7 0.3 - - - -
139A ASN* 3.0 69.9 + - - +
140A GLU 3.8 0.4 - - - -
141A ASN* 1.3 85.2 - - + +
143A ASN* 1.3 83.0 + - - +
144A ALA* 3.6 27.4 - - + -
171A MET* 3.9 19.3 - - + -
172A ASN 3.1 15.7 - - - +
173A TYR* 4.0 16.6 - + + -
174A TYR* 4.8 0.9 - - - -
30B ARG* 5.7 0.2 - - - -
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Residues in contact with ASN 143 (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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137A TYR 3.2 15.3 - - - +
138A ALA* 3.6 14.8 - - + +
139A ASN 5.4 0.4 + - - +
142A TRP* 1.3 87.6 - - - +
144A ALA* 1.3 62.2 + - - +
145A THR* 4.9 5.6 + - - +
170A ASP 4.9 1.0 - - - +
171A MET* 3.4 2.4 - - - -
172A ASN* 2.9 64.4 + - - +
174A TYR* 3.9 15.2 + - - -
25B TYR 5.6 1.0 + - - -
30B ARG* 4.3 11.3 - - - +
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Residues in contact with ALA 144 (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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136A GLY* 3.1 0.7 - - - -
137A TYR* 2.9 37.2 + - + +
142A TRP* 3.6 21.9 - - + -
143A ASN* 1.3 75.4 - - - +
145A THR* 1.3 67.7 + - - +
169A LEU* 4.8 5.6 - - + -
170A ASP 3.3 5.8 - - - -
171A MET* 3.9 19.3 - - + -
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Residues in contact with THR 145 (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 ARG* 6.0 2.4 - - - -
134A THR* 3.7 22.0 - - + -
135A ALA 3.8 6.5 - - - +
136A GLY* 4.3 3.9 - - - -
137A TYR 5.1 0.7 + - - -
143A ASN* 4.9 5.9 + - - +
144A ALA* 1.3 78.6 + - - +
146A LEU* 1.3 60.9 + - - +
147A SER* 3.6 18.7 + - - +
168A GLN 3.4 4.9 - - - +
169A LEU* 3.4 5.5 - - - +
170A ASP* 2.8 50.3 + - + +
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Residues in contact with LEU 146 (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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133A PHE 4.6 0.2 - - - -
134A THR* 3.4 0.5 - - - -
135A ALA* 2.9 41.8 + - + +
145A THR* 1.3 70.5 - - - +
147A SER* 1.3 65.2 + - - +
167A PRO* 4.1 24.2 - - + -
168A GLN 3.4 14.6 - - - +
169A LEU* 4.2 20.2 - - + +
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Residues in contact with SER 147 (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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133A PHE 3.1 9.2 - - - -
134A THR* 3.0 19.1 + - - -
145A THR* 3.6 13.7 + - - +
146A LEU* 1.3 79.5 + - - +
148A SER* 1.3 60.2 + - - +
149A LYS* 4.1 24.7 - - - -
165A ALA 4.0 0.9 - - - +
167A PRO* 3.4 9.6 - - - +
168A GLN* 2.9 41.2 + - - -
170A ASP* 5.4 2.4 + - - -
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Residues in contact with SER 148 (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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131A GLN 3.5 2.5 + - - +
132A ILE* 3.2 6.1 - - - -
133A PHE* 2.9 51.8 + - - +
147A SER* 1.3 72.9 - - - +
149A LYS* 1.3 65.7 + - - +
150A GLN* 5.3 2.4 + - - +
165A ALA 3.6 4.3 - - - -
166A GLN* 3.7 29.9 + - - +
167A PRO* 5.6 1.8 - - - -
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Residues in contact with LYS 149 (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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131A GLN 3.7 2.5 - - - -
132A ILE* 3.9 22.0 - - + -
134A THR* 5.5 0.7 - - - -
147A SER* 4.2 18.4 - - - -
148A SER* 1.3 77.0 + - - +
150A GLN* 1.3 62.2 + - - +
151A PHE* 4.3 6.6 - - + -
164A ARG* 3.5 5.0 - - - +
165A ALA* 2.8 47.4 + - + +
166A GLN* 4.8 0.3 - - - +
168A GLN* 2.9 35.1 + - - +
170A ASP* 5.0 1.0 + - - -
114B LEU* 4.0 18.2 - - + -
117B GLU* 3.0 25.0 + - - +
118B ALA* 5.7 0.4 - - - +
121B GLU* 2.8 34.2 + - - -
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Residues in contact with GLN 150 (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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131A GLN* 2.9 59.0 + - + +
148A SER* 5.3 3.0 + - - +
149A LYS* 1.3 75.8 - - - +
151A PHE* 1.3 79.1 + - - +
164A ARG* 3.9 41.0 - - + +
166A GLN* 3.6 21.6 + - - +
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Residues in contact with PHE 151 (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 TYR* 4.1 9.9 - + + -
129A ALA 3.4 4.5 - - - +
130A THR* 3.6 39.3 - - + -
131A GLN* 4.7 2.0 - - - +
132A ILE* 4.5 5.4 - - + -
149A LYS* 4.3 3.6 - - + -
150A GLN* 1.3 99.3 + - - +
152A GLN* 1.3 59.9 + - - +
153A VAL* 3.7 9.5 + - + +
159A ASN* 3.4 12.8 - - - +
162A ALA* 4.7 8.4 - - + +
163A TYR 4.3 10.7 + - - -
164A ARG* 5.2 2.0 - - - +
113B ALA* 3.7 29.8 - - + -
114B LEU* 3.5 36.8 - - + -
117B GLU* 3.8 31.0 - - + -
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Residues in contact with GLN 152 (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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106A THR 4.1 1.0 - - - +
107A ARG* 3.4 21.5 - - - +
108A VAL* 2.8 57.4 + - - +
109A SER 5.0 0.6 - - - -
110A ASP* 4.9 4.9 + - - +
128A TYR* 3.2 5.7 - - - -
129A ALA* 2.9 36.2 + - + +
131A GLN* 3.8 13.5 + - - +
151A PHE* 1.3 69.8 - - - +
153A VAL* 1.3 64.0 + - - +
154A PHE* 3.3 9.8 - - + -
159A ASN* 3.8 10.3 - - - +
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Residues in contact with VAL 153 (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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111A PRO* 5.5 0.9 - - - +
127A GLY 3.9 8.5 - - - +
128A TYR* 3.6 11.0 - - + -
151A PHE* 4.4 8.5 - - + +
152A GLN* 1.3 76.1 - - - +
154A PHE* 1.3 63.2 + - - +
155A THR* 3.1 21.5 + - + +
158A GLY* 3.6 31.6 - - - +
159A ASN* 3.3 26.3 + - - +
162A ALA* 3.8 16.8 - - + -
110B PRO* 3.4 33.7 - - + +
111B LEU* 4.7 1.1 - - + -
113B ALA* 5.0 1.6 - - + -
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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