Contacts of the strand formed by residues 159 - 174 (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 TRP 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.6 34.0 - - + +
31B ASP* 4.5 2.4 + - - -
113B LEU* 6.0 0.9 - - + -
121B ASP* 4.3 1.8 - - - -
123B GLN* 3.4 29.6 - - + -
155B PHE 4.2 6.9 - - - +
156B LEU* 3.1 33.2 + - + +
157B THR 3.6 12.6 - - - -
158B GLY* 1.3 86.7 + - - +
160B ASP* 1.3 61.6 + - - +
161B ILE* 3.9 2.6 + - - +
189B ILE* 3.4 38.4 - - + -
190B SER 3.2 25.1 - - - -
191B ARG* 3.2 55.8 - - + +
192B GLN* 2.9 17.4 + - - -
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Residues in contact with ASP 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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159B TRP* 1.3 72.0 - - - +
161B ILE* 1.3 62.4 + - - +
162B GLU* 3.4 13.5 - - - +
189B ILE* 3.3 4.4 - - - -
190B SER* 2.9 46.5 + - - +
191B ARG 5.3 0.5 - - - +
192B GLN* 2.5 39.5 + - - +
249E PRO* 5.5 0.2 - - - +
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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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23B LEU* 6.1 0.4 - - + -
26B CYS* 5.3 2.9 - - + -
150B LYS* 4.5 20.9 + - + -
154B VAL* 3.8 29.8 - - + +
155B PHE 3.6 25.8 - - - +
156B LEU* 3.9 17.7 - - + -
159B TRP 3.9 3.8 + - - +
160B ASP* 1.3 74.9 - - - +
162B GLU* 1.3 70.2 + - - +
163B SER 4.7 0.4 - - - +
187B LEU* 3.6 31.4 - - + -
189B ILE* 3.9 13.2 - - + -
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Residues in contact with GLU 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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122B SER* 5.1 0.3 + - - -
150B LYS* 4.7 10.2 + - - -
160B ASP* 3.4 19.6 + - - +
161B ILE* 1.3 82.7 - - - +
163B SER* 1.3 66.8 + - - +
188B ARG* 2.9 19.9 + - + +
189B ILE 4.2 0.3 - - - -
190B SER* 3.2 31.0 + - - -
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Residues in contact with SER 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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150B LYS* 5.9 1.6 - - - +
161B ILE* 4.0 1.3 - - - +
162B GLU* 1.3 83.1 - - - +
164B PHE* 1.3 62.3 + - - +
165B THR* 4.7 8.9 - - - +
186B GLN 3.5 2.6 - - - +
187B LEU* 3.6 4.4 - - - -
188B ARG* 2.8 52.8 + - - +
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Residues in contact with PHE 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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21B ILE* 4.0 19.1 - - + -
23B LEU* 3.7 37.0 - - + -
127B ILE* 5.0 11.2 - - + -
147B LYS* 3.5 27.7 - - - +
148B VAL* 4.5 10.9 - - - +
149B GLY 3.3 25.6 - - - +
150B LYS* 5.0 12.6 - - + +
163B SER* 1.3 71.9 - - - +
165B THR* 1.3 61.6 + - - +
185B TYR* 3.9 28.0 - + + -
186B GLN 3.0 36.1 - - - -
187B LEU* 3.8 20.6 - - + -
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Residues in contact with THR 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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147B LYS* 3.5 23.3 + - - +
163B SER* 4.7 12.6 - - - +
164B PHE* 1.3 78.3 - - - +
166B ALA* 1.3 82.1 + - - +
167B VAL* 6.3 0.2 - - + -
185B TYR* 3.4 7.7 - - - +
186B GLN* 2.7 60.3 + - + +
188B ARG* 5.6 2.0 - - + -
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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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142B ALA* 4.0 17.3 - - + -
144B ASP* 4.5 1.6 - - - +
147B LYS* 3.5 26.5 - - + +
165B THR* 1.3 93.3 + - - +
167B VAL* 1.3 64.1 + - - +
168B VAL* 3.4 11.4 + - - +
183B LEU* 6.4 0.7 - - + -
184B ASP 3.5 7.2 - - - +
185B TYR* 3.6 25.8 - - + -
186B GLN* 5.5 0.2 - - - -
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Residues in contact with VAL 167 (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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142B ALA* 4.8 1.4 - - - +
165B THR* 6.3 0.2 - - + -
166B ALA* 1.3 71.0 - - - +
168B VAL* 1.3 67.5 + - + +
169B LYS* 3.3 22.3 + - + +
183B LEU* 4.0 12.1 - - - +
184B ASP* 2.9 35.5 + - + +
186B GLN* 3.2 32.8 - - - +
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Residues in contact with VAL 168 (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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141B LEU* 3.6 21.3 - - + +
142B ALA* 4.3 19.5 + - + +
144B ASP* 3.4 32.3 - - - +
166B ALA 3.4 6.7 + - - +
167B VAL* 1.3 74.1 - - + +
169B LYS* 1.3 80.5 + - + +
170B PRO* 3.4 8.7 - - - +
183B LEU* 4.4 1.5 - - - +
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Residues in contact with LYS 169 (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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167B VAL* 3.3 19.5 + - + +
168B VAL* 1.3 94.7 - - + +
170B PRO* 1.3 77.8 - - + +
171B ALA* 3.7 1.9 + - - +
182B LYS 4.5 0.9 - - - +
183B LEU* 4.2 2.9 - - - +
184B ASP 5.5 0.7 + - - -
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Residues in contact with PRO 170 (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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139B ILE* 3.9 20.4 - - + -
140B VAL 3.3 24.2 - - - +
141B LEU* 4.2 15.3 - - + -
168B VAL 3.4 8.9 - - - +
169B LYS* 1.3 96.3 - - + +
171B ALA* 1.3 58.9 + - - +
172B ASN* 3.8 15.6 + - - +
181B SER* 4.7 4.9 - - - +
182B LYS 3.6 7.9 - - - +
183B LEU* 3.6 7.4 - - + -
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Residues in contact with ALA 171 (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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169B LYS 3.7 2.1 + - - +
170B PRO* 1.3 71.2 - - - +
172B ASN* 1.3 63.3 + - - +
173B PHE* 3.6 21.5 + - + -
181B SER* 3.5 0.5 - - - -
182B LYS* 2.6 53.1 + - + +
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Residues in contact with ASN 172 (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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139B ILE* 3.6 22.6 - - - +
170B PRO* 3.8 17.9 + - - +
171B ALA* 1.3 77.1 - - - +
173B PHE* 1.3 62.5 + - - +
174B ALA 4.1 0.2 + - - -
179B LEU* 3.7 21.6 - - + +
180B GLU 3.3 3.1 - - - -
181B SER* 2.9 26.1 + - - -
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Residues in contact with PHE 173 (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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130B ILE* 5.6 2.7 - - + -
171B ALA* 4.0 20.9 - - + -
172B ASN* 1.3 74.5 - - - +
174B ALA* 1.3 66.6 + - - +
175B LEU* 4.0 7.0 - - + +
179B LEU* 3.5 7.3 - - - +
180B GLU* 2.9 40.7 + - + +
182B LYS* 3.8 46.2 - - + -
22C TYR* 6.1 0.7 - - - -
151C ASN* 4.8 14.8 - - - -
152C ASP* 6.2 0.2 - - - -
153C ASP* 5.8 0.9 - - - -
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Residues in contact with ALA 174 (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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172B ASN 4.1 0.6 + - - -
173B PHE* 1.3 76.1 - - - +
175B LEU* 1.3 63.6 + - - +
176B GLU 4.2 0.6 + - - -
177B ASP* 5.5 0.9 - - - +
178B ARG 3.6 10.1 - - - +
179B LEU* 4.5 2.2 - - + +
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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