Contacts of the strand formed by residues 154 - 166 (chain B) in PDB entry 1L3C
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 VAL 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B MSE 4.1 23.1 - - - +
147B LEU* 3.5 29.2 - - + -
148B ARG* 3.7 28.7 + - + +
152B PHE* 3.6 15.4 + - + +
153B ASP* 1.3 74.3 - - - +
155B ASN* 1.3 72.1 + - - +
182B ILE* 3.5 30.1 - - + -
183B TYR 3.6 5.6 - - - +
184B THR* 5.1 0.4 - - + -
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B MSE 4.9 1.1 - - - -
153B ASP* 3.9 10.9 + - - +
154B VAL* 1.3 81.6 - - - +
156B ILE* 1.3 64.6 + - - +
182B ILE* 3.3 8.0 - - - +
183B TYR* 2.9 77.1 + - + +
185B GLY* 4.4 8.5 - - - +
164C GLY 6.0 0.9 - - - -
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 4.5 8.7 - - + -
144B MSE 4.0 17.9 - - + -
155B ASN* 1.3 78.7 - - - +
157B THR* 1.3 71.5 + - - +
158B GLU* 5.0 1.3 - - + -
180B ALA* 4.3 12.1 - - + -
181B LEU 3.3 9.4 - - - +
182B ILE* 3.8 22.7 - - + -
183B TYR* 4.6 0.8 + - - -
163C ARG* 3.4 3.8 - - - +
164C GLY* 2.8 50.6 + - - +
171C THR* 4.1 6.5 - - + -
173C MSE 4.0 20.6 - - + -
137D LEU* 4.2 21.8 - - + -
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Residues in contact with THR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.2 11.8 - - + +
156B ILE* 1.3 78.0 + - - +
158B GLU* 1.3 63.7 + - - +
159B LEU* 4.0 14.7 + - + +
179B VAL 3.9 0.9 - - - +
180B ALA* 3.3 1.7 - - - -
181B LEU* 2.8 37.6 + - - +
183B TYR* 3.7 21.1 + - - -
20C GLU* 3.7 28.1 + - + +
161C ILE* 3.8 15.0 - - + -
162C ALA 3.3 10.8 - - - +
163C ARG* 4.3 6.0 - - + +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LYS* 3.1 37.6 + - - +
156B ILE* 4.9 2.3 - - + +
157B THR* 1.3 71.3 - - - +
159B LEU* 1.3 62.8 + - - +
160B ASN* 4.7 8.2 + - - +
178B PRO* 3.8 19.8 - - - +
179B VAL 3.5 7.2 - - - +
180B ALA* 3.8 15.2 - - + +
160C ASN 3.6 1.0 - - - +
161C ILE* 3.4 6.9 - - - -
162C ALA* 2.7 38.5 + - + +
173C MSE 3.4 28.4 - - + +
137D LEU* 5.7 2.3 - - - +
140D LYS* 5.7 0.9 + - - -
158D GLU* 4.8 9.3 - - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 4.3 18.6 - - + +
21B VAL* 4.4 17.9 - - + -
24B LEU* 4.0 25.8 - - + -
157B THR* 4.0 9.4 - - + +
158B GLU* 1.3 81.2 - - - +
160B ASN* 1.3 62.6 + - - +
161B ILE* 4.0 20.2 + - + +
177B ASN 4.6 1.0 - - - +
178B PRO* 3.5 7.1 - - - +
179B VAL* 2.8 36.1 + - - +
181B LEU* 5.5 3.6 - - + -
20C GLU* 4.4 5.8 - - + -
159C LEU* 5.6 9.2 - - + -
160C ASN 3.7 0.9 - - - +
161C ILE* 3.7 31.9 - - + -
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASN* 5.6 10.8 - - + +
162A ALA* 5.6 0.9 - - - +
175A SER* 4.1 8.0 + - - -
158B GLU* 4.7 9.9 + - - +
159B LEU* 1.3 77.4 + - - +
161B ILE* 1.3 61.3 + - - +
176B ARG 4.7 2.7 - - - +
178B PRO* 3.5 30.8 - - - +
158C GLU 3.6 1.4 - - - +
159C LEU* 3.6 4.0 - - - +
160C ASN* 2.8 58.5 + - + +
162C ALA* 6.2 1.2 - - - +
160D ASN* 4.3 20.0 + - - +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 4.4 7.6 - - + -
20B GLU* 3.6 48.7 - - + +
21B VAL* 4.0 22.4 - - + -
159B LEU* 4.2 16.1 + - + +
160B ASN* 1.3 78.1 - - - +
162B ALA* 1.3 67.4 + - - +
163B ARG* 4.4 4.9 - - + -
175B SER* 3.6 4.2 + - - -
176B ARG* 3.1 43.3 + - + +
177B ASN 5.8 1.3 + - - +
179B VAL* 6.0 1.3 - - + -
157C THR* 3.9 17.3 - - + -
158C GLU 3.6 2.7 - - - -
159C LEU* 3.8 15.9 - - + -
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASN* 5.7 0.7 - - - +
178A PRO* 4.2 16.4 - - + -
161B ILE* 1.3 75.2 - - - +
163B ARG* 1.3 62.6 + - - +
173B MSE 3.6 27.0 - - + +
174B VAL 3.3 12.1 - - - +
175B SER* 4.3 2.5 - - - +
157C THR* 3.3 7.4 - - - +
158C GLU* 2.9 40.2 + - + +
160C ASN* 6.4 0.2 - - - +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASP* 2.9 35.6 + - - +
18B ALA* 3.5 14.3 - - - +
19B MSE 3.7 3.8 - - - +
20B GLU* 2.8 41.6 + - - +
161B ILE* 4.4 4.7 - - + +
162B ALA* 1.3 80.3 - - - +
164B GLY* 1.3 67.6 + - - +
173B MSE 3.5 2.8 - - - -
174B VAL* 2.8 37.3 + - + +
176B ARG* 2.9 45.1 - - + +
156C ILE 3.6 6.3 - - - +
157C THR* 4.4 6.1 - - - +
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ARG* 1.3 77.6 - - - +
165B ARG* 1.3 58.5 + - - +
166B ALA 4.0 1.6 + - - -
171B THR* 3.7 19.1 - - - -
172B MSE 3.4 6.7 - - - -
173B MSE 4.0 4.6 - - - +
155C ASN* 5.8 0.2 - - - +
156C ILE* 2.9 25.6 + - - +
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ARG 3.7 0.2 + - - -
164B GLY* 1.3 72.1 - - - -
166B ALA* 1.3 71.4 + - - +
167B LEU* 3.3 22.8 + - + +
171B THR* 3.5 4.0 - - - +
172B MSE 2.8 60.0 + - + +
174B VAL* 3.9 35.8 - - + +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLY 4.0 2.0 + - - -
165B ARG* 1.3 74.5 - - - +
167B LEU* 1.3 67.1 + - - +
170B GLY 4.0 3.4 - - - -
171B THR* 4.7 8.0 - - - +
148C ARG* 6.3 1.1 - - - +
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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