Contacts of the strand formed by residues 159 - 174 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.7 33.5 + - + +
31D ASP* 4.4 3.2 + - - -
113D LEU* 5.8 1.1 - - + -
121D ASP* 4.0 4.3 - - - -
123D GLN* 3.6 29.6 - - + -
155D PHE 3.6 9.9 - - - +
156D LEU* 2.8 39.2 + - + +
157D THR* 3.5 12.7 - - - -
158D GLY* 1.3 87.4 + - - +
160D ASP* 1.3 60.9 + - - +
161D ILE 3.9 0.7 + - - -
189D ILE* 3.3 30.1 - - + -
190D SER* 3.4 9.0 - - - -
191D ARG* 3.1 75.0 - - + +
192D GLN* 3.3 14.9 + - - -
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D TRP* 1.3 72.1 - - - +
161D ILE* 1.3 61.8 + - - +
162D GLU* 3.6 10.8 - - - +
189D ILE* 3.2 5.6 - - - -
190D SER* 2.8 51.3 + - - +
191D ARG 5.2 0.7 - - - +
192D GLN* 2.5 39.2 + - - +
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 6.4 0.4 - - + -
26D CYS* 4.6 7.4 - - + -
150D LYS* 4.1 23.0 + - + +
154D VAL* 3.6 34.8 - - + +
155D PHE 3.7 24.9 - - - +
156D LEU* 3.9 17.7 - - + -
159D TRP 3.9 0.4 + - - -
160D ASP* 1.3 73.2 - - - +
162D GLU* 1.3 71.8 + - - +
187D LEU* 3.6 28.9 - - + -
189D ILE* 3.9 13.5 - - + -
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D SER* 4.9 0.3 + - - -
150D LYS* 3.3 20.5 + - - -
160D ASP* 3.6 17.8 - - - +
161D ILE* 1.3 73.4 - - - +
163D SER* 1.3 63.9 + - - +
188D ARG* 2.9 23.2 + - + +
189D ILE 3.6 2.9 - - - -
190D SER* 3.3 37.4 + - - -
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Residues in contact with SER 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LYS* 4.9 1.6 - - - +
161D ILE* 4.6 0.6 - - - +
162D GLU* 1.3 83.6 - - - +
164D PHE* 1.3 61.8 + - - +
165D THR* 4.4 10.1 - - - +
186D GLN 3.4 4.0 - - - +
187D LEU* 3.7 4.7 - - - -
188D ARG* 3.0 39.6 + - - +
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Residues in contact with PHE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 3.4 39.5 - - + -
23D LEU* 3.6 35.4 - - + -
127D ILE* 4.8 11.4 - - + -
147D LYS* 3.6 27.7 - - - +
148D VAL* 5.1 3.2 - - - -
149D GLY 3.2 26.5 - - - +
150D LYS* 5.0 11.1 - - + +
163D SER* 1.3 72.5 - - - +
165D THR* 1.3 61.4 + - - +
185D TYR* 4.1 27.6 - + + -
186D GLN 3.4 21.1 - - - -
187D LEU* 3.8 21.1 - - + +
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Residues in contact with THR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ASP* 5.2 0.2 + - - -
147D LYS* 3.5 22.7 + - - +
163D SER* 4.4 15.9 - - - +
164D PHE* 1.3 76.5 - - - +
166D ALA* 1.3 86.8 + - - +
185D TYR* 3.3 9.4 - - - +
186D GLN* 2.8 52.2 + - + +
188D ARG* 5.7 2.7 - - + -
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA* 3.8 21.9 - - + +
144D ASP* 4.3 7.1 - - - +
147D LYS* 3.8 14.5 - - + +
165D THR* 1.3 91.4 + - - +
167D VAL* 1.3 64.6 + - - +
168D VAL* 3.4 10.0 + - - +
183D LEU* 6.0 0.4 - - + -
184D ASP 3.7 6.1 - - - +
185D TYR* 3.7 30.7 - - + +
186D GLN* 6.0 0.2 - - - -
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Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA* 4.7 1.4 - - - +
165D THR* 5.8 0.2 - - - +
166D ALA* 1.3 70.7 - - - +
168D VAL* 1.3 68.5 + - + +
169D LYS* 3.3 19.1 + - + +
183D LEU* 3.5 20.4 - - - +
184D ASP* 2.9 38.9 + - + +
186D GLN* 3.6 26.0 - - - +
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Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.7 20.8 - - + +
142D ALA* 4.5 14.3 + - + +
144D ASP* 3.8 24.7 - - - +
166D ALA 4.3 7.2 - - - +
167D VAL* 1.3 76.1 - - + +
169D LYS* 1.3 77.8 + - + +
170D PRO* 3.2 12.6 - - - +
183D LEU* 4.3 3.3 - - - +
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Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D VAL* 3.4 19.1 - - + +
168D VAL* 1.3 90.0 - - + +
170D PRO* 1.3 76.8 - - + +
171D ALA* 3.7 1.6 + - - +
182D LYS 4.7 0.3 - - - +
183D LEU* 4.4 1.0 - - - +
184D ASP 5.7 0.5 + - - -
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Residues in contact with PRO 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ILE* 4.1 12.8 - - + -
140D VAL 3.3 25.4 - - - +
141D LEU* 4.2 13.5 - - + -
168D VAL 3.2 10.5 - - - +
169D LYS* 1.3 94.0 - - + +
171D ALA* 1.3 60.6 + - - +
172D ASN* 3.5 20.3 + - - +
181D SER* 4.6 4.7 - - - +
182D LYS 3.3 13.0 - - - +
183D LEU* 3.7 8.9 - - + -
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Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LYS 3.7 2.0 + - - +
170D PRO* 1.3 69.7 - - - +
172D ASN* 1.3 63.9 + - - +
173D PHE* 3.6 16.4 + - + -
180D GLU 3.8 0.2 - - - +
182D LYS* 2.7 54.2 + - + +
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Residues in contact with ASN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ILE* 3.5 30.7 - - - +
170D PRO* 3.5 20.3 + - - +
171D ALA* 1.3 75.7 - - - +
173D PHE* 1.3 64.0 + - - +
174D ALA 4.1 0.2 + - - -
179D LEU* 3.8 18.1 - - + +
180D GLU 3.6 2.9 - - - -
181D SER* 3.0 19.4 + - - -
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Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ILE* 5.6 2.9 - - + -
171D ALA* 4.0 19.3 - - + -
172D ASN* 1.3 74.5 - - - +
174D ALA* 1.3 68.6 + - - +
175D LEU* 4.7 16.2 - - + +
179D LEU* 3.3 11.8 - - - +
180D GLU* 2.9 40.1 + - + +
182D LYS* 3.8 44.0 - - + -
22E TYR* 5.9 0.9 - - - -
151E ASN* 4.1 20.9 - - - -
153E ASP* 5.6 1.6 - - - -
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Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ASN 4.1 0.6 + - - -
173D PHE* 1.3 76.3 - - - +
175D LEU* 1.3 65.0 + - - +
176D GLU 4.3 0.5 + - - -
177D ASP 5.6 0.7 - - - +
178D ARG 3.4 9.2 - - - +
179D LEU* 4.3 3.6 - - + +
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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