Contacts of the strand formed by residues 179 - 191 (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 LEU 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D ARG* 4.2 0.2 - - - +
133D SER* 3.1 35.2 + - - +
137D ARG* 3.5 46.0 - - + +
138D ASN 4.4 8.5 - - - +
139D ILE* 5.3 3.8 - - + -
172D ASN* 3.8 28.5 - - + +
173D PHE 3.3 24.9 - - - +
174D ALA* 4.3 3.1 - - + +
178D ARG* 1.3 75.5 - - - +
180D GLU* 1.3 79.4 + - - +
181D SER* 4.4 1.8 - - - +
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Residues in contact with GLU 180 (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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76D ARG* 2.8 26.5 + - - -
130D ILE* 3.6 21.3 - - + +
131D VAL 3.2 5.9 - - - +
132D ARG* 2.9 50.8 + - + +
138D ASN 5.5 0.4 - - - -
171D ALA 3.8 0.5 - - - +
173D PHE* 2.9 45.2 + - + +
175D LEU* 3.7 25.8 - - + +
178D ARG 4.0 0.4 + - - +
179D LEU* 1.3 87.6 - - - +
181D SER* 1.3 60.9 + - - +
41E PHE* 4.1 4.2 - - - -
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Residues in contact with SER 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ILE* 2.9 23.9 - - - -
131D VAL* 3.0 15.7 + - - -
138D ASN 3.5 17.6 + - - -
139D ILE* 3.6 6.6 - - - +
140D VAL* 3.2 34.4 - - - +
170D PRO* 4.7 0.7 - - - -
171D ALA 3.7 2.0 - - - -
172D ASN* 3.0 29.6 + - - -
179D LEU* 4.4 0.7 - - - +
180D GLU* 1.3 73.9 - - - +
182D LYS* 1.3 59.6 + - - +
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Residues in contact with LYS 182 (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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78D VAL* 4.4 16.3 - - - +
128D TYR* 3.6 46.5 - - + -
129D LEU 3.3 3.8 - - - -
130D ILE* 3.4 17.5 - - + -
169D LYS 4.7 0.3 - - - +
170D PRO* 3.3 4.3 - - - +
171D ALA* 2.7 52.4 + - + +
173D PHE* 3.8 32.8 - - + -
181D SER* 1.3 73.4 - - - +
183D LEU* 1.3 66.2 + - - +
184D ASP* 4.3 2.1 + - + -
151E ASN* 5.0 6.7 - - - +
153E ASP* 3.9 18.8 + - - -
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Residues in contact with LEU 183 (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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19D THR* 3.4 26.0 - - + +
127D ILE 3.6 1.7 - - - +
128D TYR* 3.1 11.7 - - - -
129D LEU* 2.9 34.7 + - + +
140D VAL* 3.9 16.2 - - + +
141D LEU* 3.6 28.7 - - - +
142D ALA* 3.6 8.5 - - + +
166D ALA* 6.0 0.9 - - + -
167D VAL 3.5 23.1 - - - +
168D VAL 4.3 5.4 - - - +
170D PRO* 3.7 28.0 - - + -
182D LYS* 1.3 75.0 - - - +
184D ASP* 1.3 59.9 + - - +
185D TYR* 3.9 16.1 - - + +
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Residues in contact with ASP 184 (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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126D HIS* 3.1 29.8 + - - +
128D TYR* 3.3 32.3 + - + -
166D ALA* 3.7 0.2 - - - -
167D VAL* 2.9 44.6 + - + +
169D LYS 5.7 0.6 + - - -
182D LYS* 4.3 2.2 + - + -
183D LEU* 1.3 74.6 - - - +
185D TYR* 1.3 64.8 + - - +
186D GLN* 3.6 17.6 + - - +
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Residues in contact with TYR 185 (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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19D THR* 2.4 32.8 + - - -
20D GLY* 3.6 9.0 + - - -
21D ILE* 3.4 40.7 - - + +
126D HIS* 3.3 5.9 - - - -
127D ILE* 2.9 53.6 + - + +
129D LEU* 4.2 17.0 - - + +
142D ALA* 4.8 2.4 - - - +
147D LYS* 4.6 8.3 - - + -
164D PHE* 4.1 15.7 - + + -
165D THR 3.3 9.2 - - - +
166D ALA* 3.7 23.8 - - + +
183D LEU* 3.9 25.9 - - + +
184D ASP* 1.3 80.0 - - - +
186D GLN* 1.3 61.0 + - - +
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Residues in contact with GLN 186 (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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124D THR* 4.0 11.0 + - - +
125D LEU 3.3 5.8 - - - +
126D HIS* 3.5 28.1 - - - +
163D SER 3.4 2.9 - - - +
164D PHE* 3.4 7.7 - - - -
165D THR* 2.8 55.3 + - + +
167D VAL* 3.6 19.5 - - + +
184D ASP* 3.6 18.4 + - - +
185D TYR* 1.3 79.1 - - - +
187D LEU* 1.3 59.5 + - - +
188D ARG* 3.9 14.1 + - + +
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Residues in contact with LEU 187 (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* 3.9 10.1 - - + -
26D CYS* 3.5 32.1 - - - -
36D PHE* 5.0 5.8 - - + -
124D THR* 3.5 1.3 - - - -
125D LEU* 2.9 63.5 + - + +
127D ILE* 6.4 1.3 - - + -
150D LYS* 6.0 0.4 - - + -
156D LEU* 4.3 8.1 - - + -
161D ILE* 3.6 27.8 - - + -
163D SER 3.8 6.5 - - - +
164D PHE* 3.8 28.4 - - + -
186D GLN* 1.3 73.2 - - - +
188D ARG* 1.3 61.2 - - - +
189D ILE* 3.7 9.6 + - + -
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Residues in contact with ARG 188 (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* 5.4 9.9 + - - -
123D GLN 3.5 8.2 + - - -
124D THR* 3.4 41.0 + - - +
161D ILE* 3.9 0.9 - - - +
162D GLU* 2.9 32.9 + - + +
163D SER* 3.0 31.1 + - - +
165D THR* 5.7 2.0 - - + -
186D GLN* 4.6 15.8 + - + +
187D LEU* 1.3 72.0 - - - +
189D ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 189 (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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29D LEU* 3.6 27.8 - - + -
122D SER* 3.4 6.1 - - - -
123D GLN* 2.8 45.7 + - + +
125D LEU* 4.2 8.3 - - + -
156D LEU* 3.6 23.8 - - + -
159D TRP* 3.3 29.2 - - + -
160D ASP 3.2 14.1 - - - +
161D ILE* 3.9 13.0 - - + -
162D GLU* 3.6 4.0 - - - -
187D LEU* 4.1 16.4 - - + +
188D ARG* 1.3 80.6 - - - +
190D SER* 1.3 61.2 + - - +
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Residues in contact with SER 190 (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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120D PHE 5.7 1.1 - - - -
122D SER* 3.1 24.2 - - - +
159D TRP* 3.4 4.0 - - - -
160D ASP* 2.8 48.9 + - - +
162D GLU* 3.3 18.5 + - - -
189D ILE* 1.3 71.8 - - - +
191D ARG* 1.3 66.4 + - - +
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Residues in contact with ARG 191 (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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31D ASP* 3.0 34.8 + - - -
115D PHE* 4.2 6.3 - - - -
118D TYR* 3.2 28.5 - - - -
119D PRO* 3.0 28.5 + - - +
120D PHE 4.7 3.5 - - - +
121D ASP* 2.8 45.4 + - - +
158D GLY 4.1 4.3 - - - +
159D TRP* 3.1 40.2 - - + +
160D ASP* 5.2 0.9 - - - +
190D SER* 1.3 78.6 + - - +
192D GLN* 1.3 76.1 + - - +
193D TYR* 3.4 15.4 + - - +
196D TYR* 4.3 20.6 + - + -
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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