Contacts of the helix formed by residues 132 - 149 (chain A) in PDB entry 3L49
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 ASN 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 1.3 70.6 - - - +
133A ASN* 1.3 57.5 + - - +
134A TYR* 3.3 19.2 + - - +
135A SER* 3.0 35.0 + - - +
136A ILE* 3.0 33.1 + - + +
299A PHE* 3.8 36.1 - - + +
300A ALA 4.4 2.4 + - - -
302A ALA* 5.9 0.6 - - - +
138B ALA* 5.4 0.2 - - - +
139B GLU* 3.6 22.0 - - - +
142B LEU* 3.8 6.0 - - - +
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Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 5.0 0.4 + - - -
130A THR* 3.3 17.2 + - - +
131A SER* 3.1 27.1 + - - +
132A ASN* 1.3 72.0 + - - +
134A TYR* 1.3 61.0 + - + +
135A SER 3.5 0.2 - - - -
136A ILE* 3.9 12.5 - - - +
137A GLY* 2.8 28.4 + - - -
165A VAL* 3.6 19.1 - - - +
168A ILE* 3.6 33.7 - - + +
169A ARG* 2.8 44.5 + - + +
172A GLN* 4.3 0.2 - - - +
272A GLN* 4.4 0.7 + - - +
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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
----------------------------------------------------------
132A ASN* 3.2 14.3 - - - +
133A ASN* 1.3 80.2 - - + +
135A SER* 1.3 64.3 + - - +
138A ALA* 3.2 13.9 + - - +
168A ILE* 3.8 33.9 - - + +
172A GLN* 2.6 28.9 + - - +
299A PHE* 4.9 6.5 - + - -
134B TYR 5.4 0.6 - - - +
138B ALA* 3.7 18.4 - - + -
142B LEU* 3.8 26.9 - - + -
172B GLN* 5.1 0.9 - - - -
175B TYR* 3.5 37.3 + + - -
176B VAL* 3.9 25.8 + - + +
179B ALA* 3.8 24.1 - - - +
180B PHE* 5.1 2.5 - + - -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASN* 3.0 32.9 + - - -
134A TYR* 1.3 73.4 - - - +
136A ILE* 1.3 59.8 + - - +
138A ALA* 3.1 3.9 + - - +
139A GLU* 2.8 55.4 + - - +
135B SER* 4.1 15.4 + - - +
138B ALA* 5.0 1.6 - - - +
139B GLU* 3.3 19.3 + - - +
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.7 21.1 - - - -
132A ASN* 3.0 21.9 + - + +
133A ASN* 3.9 13.2 - - - +
135A SER* 1.3 78.9 - - - +
137A GLY* 1.3 64.2 - - - +
139A GLU* 4.2 4.2 - - - +
140A LEU* 3.1 26.3 + - - +
169A ARG* 4.5 6.5 - - + -
249A VAL* 3.9 21.3 - - + -
270A ALA* 3.7 26.9 - - + +
272A GLN* 4.5 8.7 - - + -
302A ALA* 3.7 32.1 - - + -
303A VAL 6.4 0.7 - - - -
304A LEU* 5.6 0.3 - - - +
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASN 2.8 23.3 + - - -
135A SER 3.3 0.2 - - - -
136A ILE* 1.3 77.3 - - - +
138A ALA* 1.3 61.1 + - - +
140A LEU* 4.2 4.1 - - - +
141A ALA* 3.3 23.0 + - - +
169A ARG* 4.2 17.9 - - - +
172A GLN* 3.6 16.0 - - - +
173A MET* 4.2 3.8 + - - +
222A TRP* 5.5 2.2 + - - -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR 3.2 17.7 + - - +
135A SER* 3.1 5.7 + - - +
137A GLY* 1.3 74.5 - - - +
139A GLU* 1.3 54.8 + - - +
141A ALA* 3.1 4.5 + - - +
142A LEU* 2.8 41.8 + - + +
172A GLN* 3.6 11.9 - - + +
176A VAL* 4.2 10.9 - - + +
134B TYR* 3.7 34.3 - - + -
135B SER* 5.0 2.9 - - - +
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 2.8 33.1 + - - +
136A ILE* 4.2 3.6 - - - +
138A ALA* 1.3 72.5 - - - +
140A LEU* 1.3 57.2 + - - +
142A LEU* 3.3 7.7 + - - +
143A GLN* 2.8 30.7 + - - +
304A LEU* 4.1 29.3 + - + +
132B ASN* 3.6 20.9 - - - +
135B SER* 3.1 18.2 + - - +
139B GLU* 5.2 1.0 - - - +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE 3.1 17.9 + - - +
137A GLY* 4.2 4.0 - - - +
139A GLU* 1.3 75.4 - - - +
141A ALA* 1.3 62.6 + - - +
143A GLN* 3.2 4.8 + - - +
144A MET* 3.0 23.2 + - - +
222A TRP* 3.7 26.5 - - + +
223A ALA 4.6 0.4 - - - +
247A TYR* 4.1 12.6 - - + -
248A GLY* 3.5 37.0 - - - +
249A VAL* 3.8 18.6 - - + -
268A ALA* 3.9 19.5 - - + +
270A ALA* 4.3 3.8 - - + +
304A LEU* 3.8 26.3 - - + +
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Residues in contact with ALA 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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137A GLY 3.3 13.2 + - - +
138A ALA 3.1 8.4 + - - +
140A LEU* 1.3 77.6 - - - +
142A LEU* 1.3 61.7 + - - +
144A MET* 3.3 15.7 + - - +
145A VAL* 3.1 25.3 + - - +
173A MET* 3.7 33.0 - - + +
176A VAL* 3.9 16.1 - - + +
177A LEU* 4.7 5.2 - - + +
222A TRP* 5.4 0.8 - - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA* 2.8 29.6 + - + +
139A GLU* 3.6 6.1 - - - +
141A ALA* 1.3 69.3 - - - +
143A GLN* 1.3 61.4 + - - +
145A VAL* 3.3 7.4 - - + +
146A ALA* 2.9 23.9 + - - +
176A VAL* 4.1 15.3 - - + -
180A PHE* 4.8 5.2 - - + -
132B ASN* 3.6 28.0 - - - +
134B TYR* 3.9 30.1 - - + -
297B PHE* 3.3 37.9 - - + -
299B PHE* 3.8 19.3 - - + -
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Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU 2.8 15.1 + - - +
140A LEU* 3.4 11.0 - - - +
142A LEU* 1.3 76.8 - - - +
144A MET* 1.3 55.6 + - - +
146A ALA* 3.4 9.7 + - - +
147A ASP* 2.9 64.7 + - - +
247A TYR* 4.4 0.7 - - + -
268A ALA* 4.0 15.3 - - + -
304A LEU* 3.5 19.2 - - + +
306A THR* 3.6 30.3 + - + +
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Residues in contact with MET 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU 3.0 14.2 + - - +
141A ALA* 3.3 15.2 + - - +
143A GLN* 1.3 76.9 - - - +
145A VAL* 1.3 56.3 + - - +
147A ASP* 3.4 2.9 + - - +
148A LEU* 2.9 37.5 + - + +
154A VAL* 4.0 22.7 - - + -
173A MET* 4.9 5.2 - - + -
177A LEU* 5.8 4.9 - - + -
220A ALA* 3.7 24.0 - - + -
221A ILE 4.9 0.4 - - - +
222A TRP* 3.2 37.2 - - + -
247A TYR* 3.5 46.7 + - + -
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Residues in contact with VAL 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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141A ALA 3.1 15.1 + - - +
142A LEU* 3.3 20.4 - - - +
144A MET* 1.3 73.9 - - - +
146A ALA* 1.3 59.4 + - - +
148A LEU* 3.6 7.4 - - - -
149A GLY 2.9 22.3 + - - -
150A GLY* 3.0 18.1 + - - -
176A VAL* 4.4 5.2 - - + -
177A LEU* 5.2 3.8 - - + -
180A PHE* 3.6 48.7 - - + -
183A VAL* 3.7 24.9 - - + -
296B PRO* 4.1 2.0 - - + +
297B PHE* 4.0 10.1 - - + -
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Residues in contact with ALA 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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142A LEU 2.9 17.1 + - - +
143A GLN* 3.5 15.9 - - - +
145A VAL* 1.3 77.2 - - - +
147A ASP* 1.3 58.1 + - - +
149A GLY* 3.1 14.4 + - - -
295B LYS* 3.4 35.0 - - + +
296B PRO* 4.4 12.1 - - + -
297B PHE* 3.9 16.1 - - + +
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Residues in contact with ASP 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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143A GLN* 2.9 40.0 + - - +
144A MET 3.7 1.3 - - - +
146A ALA* 1.3 75.6 - - - +
148A LEU* 1.3 61.3 + - - +
149A GLY 3.5 0.3 + - - -
245A ARG* 5.4 6.0 - - + +
247A TYR* 2.7 39.1 + - - +
267A GLY* 4.3 7.4 - - - +
306A THR* 5.7 0.7 - - - -
295B LYS* 5.1 8.2 + - - +
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Residues in contact with LEU 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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144A MET* 2.9 26.8 + - + +
145A VAL* 3.7 6.7 - - - +
146A ALA 3.3 0.2 - - - -
147A ASP* 1.3 75.5 - - + +
149A GLY* 1.3 60.0 + - - +
150A GLY 4.2 2.0 - - - +
151A LYS* 3.1 34.5 + - - +
152A GLY* 4.2 9.2 - - - +
154A VAL* 4.0 26.5 - - + -
183A VAL* 4.0 17.7 - - + -
219A GLY* 3.8 35.0 - - - +
220A ALA* 4.2 8.3 - - + -
247A TYR* 6.0 0.7 - - + +
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL 2.9 4.6 + - - -
146A ALA 3.1 14.6 + - - -
147A ASP 3.2 1.0 + - - -
148A LEU* 1.3 78.3 - - - +
150A GLY* 1.3 59.6 + - - +
151A LYS* 3.3 4.4 + - - +
295B LYS* 5.3 2.9 - - - -
296B PRO* 4.0 19.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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