Contacts of the strand formed by residues 179 - 191 (chain B) in PDB entry 4LML
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 LEU 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 4.1 0.2 - - - +
133B SER* 3.2 30.7 + - - +
137B ARG* 3.5 47.6 - - + +
138B ASN 4.6 5.8 - - - +
139B ILE* 5.6 2.5 - - + -
172B ASN* 3.7 29.4 - - + +
173B PHE 3.5 11.0 - - - +
174B ALA* 4.5 2.9 - - + +
178B ARG* 1.3 75.7 - - - +
180B GLU* 1.3 92.0 + - - +
181B SER* 4.2 2.9 - - - +
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Residues in contact with GLU 180 (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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76B ARG* 2.7 26.5 + - - -
130B ILE* 3.4 22.9 - - + +
131B VAL 3.1 7.1 - - - +
132B ARG* 3.1 51.7 + - + +
172B ASN* 3.3 0.5 - - - -
173B PHE* 2.9 44.1 + - + +
175B LEU* 4.0 14.4 - - + +
178B ARG 3.9 0.6 + - - -
179B LEU* 1.3 82.2 - - - +
181B SER* 1.3 61.5 + - - +
41C PHE* 3.5 21.8 - - - -
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU 3.3 1.9 - - - +
130B ILE* 3.0 6.3 - - - -
131B VAL* 2.9 32.6 + - - -
138B ASN 3.2 23.3 + - - -
139B ILE* 3.5 6.4 - - - +
140B VAL* 3.6 26.7 - - - +
170B PRO* 4.8 2.9 - - - -
171B ALA 3.5 3.6 - - - -
172B ASN* 2.9 27.1 + - - -
179B LEU* 4.2 0.5 - - - +
180B GLU* 1.3 71.1 - - - +
182B LYS* 1.3 58.5 + - - +
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.0 26.7 - - - +
128B TYR* 3.8 36.8 - - + -
129B LEU 3.2 4.0 - - - +
130B ILE* 3.5 16.6 - - + -
169B LYS 4.5 0.9 - - - +
170B PRO* 3.6 3.0 - - - +
171B ALA* 2.6 51.7 + - + +
173B PHE* 3.8 34.3 - - + -
181B SER* 1.3 73.2 - - - +
183B LEU* 1.3 66.6 + - - +
184B ASP* 6.0 0.7 - - + -
151C ASN* 4.8 7.7 - - - +
153C ASP* 3.7 21.8 + - - -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.5 26.5 - - + +
127B ILE 3.6 1.4 - - - +
128B TYR* 3.2 8.7 - - - +
129B LEU* 2.9 36.9 + - + +
140B VAL* 3.6 24.5 - - + +
141B LEU* 3.6 30.1 - - - +
142B ALA* 3.9 5.2 - - + +
166B ALA* 6.4 0.7 - - + -
167B VAL 4.0 16.4 - - - +
168B VAL 4.4 2.9 - - - +
169B LYS 4.2 0.9 - - - +
170B PRO* 3.6 29.2 - - + -
182B LYS* 1.3 74.8 - - - +
184B ASP* 1.3 60.3 + - - +
185B TYR* 3.9 15.3 - - + -
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Residues in contact with ASP 184 (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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126B HIS* 3.3 22.5 + - - +
128B TYR* 3.3 27.8 + - + -
166B ALA* 3.5 1.0 - - - -
167B VAL* 2.9 46.3 + - + +
169B LYS 5.5 0.8 + - - -
182B LYS* 6.0 0.7 - - + -
183B LEU* 1.3 77.2 - - - +
185B TYR* 1.3 72.9 + - - +
186B GLN* 3.6 19.8 + - - -
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Residues in contact with TYR 185 (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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19B THR* 2.4 33.4 + - - -
20B GLY* 3.3 15.2 + - - -
21B ILE* 3.6 30.3 - - + -
125B LEU 3.6 0.2 - - - +
126B HIS* 3.4 2.4 - - - -
127B ILE* 2.9 50.8 + - + +
129B LEU* 4.0 21.1 - - + -
142B ALA* 4.5 4.0 - - + +
147B LYS* 3.9 14.1 - - + -
164B PHE* 3.9 29.2 - + + -
165B THR 3.4 5.6 - - - +
166B ALA* 3.6 24.2 - - + +
183B LEU* 4.3 16.2 - - + -
184B ASP* 1.3 81.7 - - - +
186B GLN* 1.3 59.4 + - - +
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Residues in contact with GLN 186 (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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124B THR* 4.3 14.3 + - - +
125B LEU 3.3 5.4 - - - +
126B HIS* 3.9 16.8 + - + -
163B SER 3.5 1.9 - - - +
164B PHE* 3.0 8.8 - - - -
165B THR* 2.7 57.9 + - + +
167B VAL* 3.2 27.8 - - + +
184B ASP* 3.6 18.0 + - - +
185B TYR* 1.3 78.9 - - - +
187B LEU* 1.3 59.6 + - - +
188B ARG* 4.0 16.9 + - + +
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Residues in contact with LEU 187 (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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23B LEU* 4.2 10.5 - - + -
26B CYS* 4.2 25.4 - - + -
36B PHE* 5.1 6.1 - - + -
123B GLN 3.8 0.2 - - - +
124B THR* 3.5 1.3 - - - -
125B LEU* 2.9 54.9 + - + +
127B ILE* 6.2 2.4 - - + +
150B LYS* 5.8 0.2 - - + -
156B LEU* 4.2 19.5 - - + -
161B ILE* 3.6 28.3 - - + -
163B SER 3.7 8.5 - - - +
164B PHE* 3.8 25.7 - - + -
186B GLN* 1.3 72.8 - - - +
188B ARG* 1.3 63.4 + - - +
189B ILE* 3.6 10.7 + - + +
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Residues in contact with ARG 188 (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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122B SER* 5.3 11.8 + - - -
123B GLN 3.6 7.1 + - - +
124B THR* 3.7 39.0 + - - +
161B ILE* 4.2 0.7 - - - +
162B GLU* 2.9 30.2 + - + +
163B SER* 2.8 36.7 + - - +
165B THR* 5.6 1.8 - - + -
186B GLN* 4.0 19.1 + - + +
187B LEU* 1.3 73.9 - - - +
189B ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 189 (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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29B LEU* 3.5 28.5 - - + -
122B SER* 3.3 5.1 - - - -
123B GLN* 2.8 40.2 + - + +
125B LEU* 3.7 15.7 - - + -
156B LEU* 3.8 9.4 - - + -
159B TRP* 3.4 29.1 - - + -
160B ASP 3.3 7.4 - - - +
161B ILE* 3.9 26.5 - - + -
162B GLU* 4.2 2.7 - - - +
187B LEU* 3.9 23.6 - - + +
188B ARG* 1.3 79.9 - - - +
190B SER* 1.3 60.2 + - - +
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Residues in contact with SER 190 (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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120B PHE 5.1 2.2 - - - -
121B ASP 3.8 4.5 - - - -
122B SER* 3.1 25.1 - - - -
159B TRP* 3.2 5.0 - - - -
160B ASP* 2.9 42.8 + - - +
162B GLU* 3.2 17.2 + - - -
189B ILE* 1.3 72.9 - - - +
191B ARG* 1.3 67.5 + - - +
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Residues in contact with ARG 191 (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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31B ASP* 2.7 32.3 + - - -
114B ASP 4.6 0.2 + - - -
115B PHE* 4.3 10.3 - - - -
118B TYR* 3.7 27.2 - - - +
119B PRO* 2.7 34.7 + - + +
120B PHE 4.3 3.5 - - - +
121B ASP* 2.8 40.0 + - - +
123B GLN* 4.1 5.7 - - - +
158B GLY 4.4 4.3 - - - +
159B TRP* 3.2 37.4 - - + +
160B ASP* 5.3 0.7 - - - +
190B SER* 1.3 76.9 + - - +
192B GLN* 1.3 74.2 + - - +
193B TYR* 3.4 16.0 + - - +
196B TYR* 4.2 18.3 + - + -
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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