Contacts of the strand formed by residues 179 - 191 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C VAL 4.1 0.2 - - - +
132C ARG* 3.9 0.3 - - - +
133C SER* 3.0 47.0 + - - +
137C ARG* 3.5 40.8 - - + +
138C ASN 3.7 17.5 - - - +
139C ILE* 5.0 3.6 - - + -
172C ASN* 4.8 12.8 - - + +
173C PHE 3.4 10.5 - - - +
174C ALA* 4.6 2.7 - - + +
178C ARG* 1.3 75.7 - - - +
180C GLU* 1.3 72.0 + - - +
181C SER* 4.4 4.3 - - - +
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Residues in contact with GLU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.0 7.8 - - - -
76C ARG* 3.3 18.8 + - - -
130C ILE* 3.4 22.5 - - + +
131C VAL 3.1 11.0 - - - +
132C ARG* 3.5 43.1 + - + +
171C ALA 3.9 0.3 - - - +
172C ASN* 3.4 5.9 - - - +
173C PHE* 2.9 45.2 + - + +
175C LEU* 4.0 25.7 - - + +
178C ARG 4.0 2.9 + - - +
179C LEU* 1.3 82.5 - - - +
181C SER* 1.3 64.4 + - - +
182C LYS* 5.7 0.2 - - - -
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU 3.6 1.0 - - - +
130C ILE* 3.0 6.4 - - - +
131C VAL* 3.0 35.0 + - - -
138C ASN 3.2 19.6 + - - -
139C ILE* 3.3 18.3 - - - +
140C VAL* 3.6 29.2 - - - +
170C PRO* 5.0 1.6 - - - -
171C ALA 3.9 3.1 - - - -
172C ASN* 3.6 14.5 + - - -
179C LEU* 4.4 1.6 - - - +
180C GLU* 1.3 72.3 - - - +
182C LYS* 1.3 60.7 + - - +
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Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASN* 5.1 6.8 + - - +
153A ASP* 3.9 19.4 + - - -
78C VAL* 4.2 25.5 - - - +
128C TYR* 4.1 26.0 - - + -
129C LEU 3.4 3.6 - - - +
130C ILE* 3.5 16.4 - - + -
140C VAL* 4.1 0.6 - - - +
169C LYS 4.8 0.2 - - - +
170C PRO* 3.4 6.1 - - - +
171C ALA* 2.9 47.7 + - + +
173C PHE* 3.8 33.9 - - + -
181C SER* 1.3 75.6 - - - +
183C LEU* 1.3 74.2 + - - +
184C ASP* 6.0 0.4 - - + -
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR* 3.5 25.6 - - + +
127C ILE 3.9 0.2 - - - +
128C TYR* 3.3 8.1 - - - +
129C LEU* 2.9 36.9 + - + +
140C VAL* 3.7 19.1 - - + +
141C LEU* 3.6 29.2 - - - +
142C ALA* 3.8 6.3 - - + +
166C ALA* 6.4 0.2 - - + -
167C VAL 3.6 20.6 - - - +
168C VAL 4.2 3.4 - - - +
169C LYS 4.1 1.1 - - - +
170C PRO* 3.5 35.4 - - + -
182C LYS* 1.3 75.1 - - - +
184C ASP* 1.3 59.9 + - - +
185C TYR* 3.9 15.7 + - + -
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Residues in contact with ASP 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C HIS* 3.2 22.1 + - - +
127C ILE 4.2 0.2 - - - +
128C TYR* 3.4 30.4 + - + -
166C ALA* 3.8 0.4 - - - -
167C VAL* 3.1 42.4 + - + +
169C LYS 5.7 0.8 + - - -
182C LYS* 6.0 0.7 - - + -
183C LEU* 1.3 74.7 - - - +
185C TYR* 1.3 78.2 + - - +
186C GLN* 3.5 18.6 + - - +
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Residues in contact with TYR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR* 2.5 32.1 + - - -
20C GLY* 3.3 14.9 + - - -
21C ILE* 3.8 26.9 - - + -
126C HIS* 3.4 1.7 - - - -
127C ILE* 2.9 46.8 + - + +
129C LEU* 3.9 24.9 - - + -
142C ALA* 4.6 4.4 - - + +
147C LYS* 4.2 10.2 - - + +
164C PHE* 3.7 30.1 - + + -
165C THR 3.7 3.4 - - - -
166C ALA* 3.5 26.5 - - + +
183C LEU* 4.3 18.4 - - + -
184C ASP* 1.3 88.2 - - - +
186C GLN* 1.3 60.6 + - - +
187C LEU 4.4 0.2 + - - -
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Residues in contact with GLN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C THR* 4.2 13.0 + - - +
125C LEU 3.4 3.8 - - - -
126C HIS* 4.0 13.7 - - - +
163C SER 3.5 2.6 - - - +
164C PHE* 3.1 9.2 - - - -
165C THR* 2.9 49.8 + - + +
166C ALA* 6.0 0.4 - - - -
167C VAL* 3.4 26.0 - - + +
184C ASP* 3.5 21.7 + - - +
185C TYR* 1.3 80.7 - - - +
187C LEU* 1.3 60.8 + - - +
188C ARG* 3.9 12.3 + - + +
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Residues in contact with LEU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.9 12.8 - - + -
26C CYS* 3.7 30.1 - - - -
36C PHE* 4.6 16.4 - - + -
38C VAL* 6.2 0.2 - - + -
124C THR* 4.5 0.2 - - - -
125C LEU* 2.9 45.7 + - + +
127C ILE* 6.1 3.8 - - + -
150C LYS* 5.5 0.4 - - + -
156C LEU* 4.7 14.1 - - + -
161C ILE* 3.8 27.4 - - + -
163C SER 4.2 1.3 - - - +
164C PHE* 3.8 30.3 - - + -
185C TYR 4.3 0.4 - - - -
186C GLN* 1.3 73.2 - - - +
188C ARG* 1.3 61.4 + - - +
189C ILE* 3.6 10.8 + - + +
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Residues in contact with ARG 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C SER* 5.7 6.5 - - - -
123C GLN 3.7 7.1 + - - -
124C THR* 3.4 42.0 + - - +
161C ILE* 3.9 1.0 - - - +
162C GLU* 2.8 32.6 + - + +
163C SER* 2.8 37.3 + - - +
165C THR* 5.9 2.2 - - + -
186C GLN* 4.8 14.2 + - + +
187C LEU* 1.3 71.0 - - - +
189C ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 3.6 28.7 - - + -
122C SER* 3.7 2.9 - - - -
123C GLN* 2.8 45.0 + - + +
125C LEU* 3.7 11.0 - - + -
156C LEU* 3.6 25.1 - - + -
159C TRP* 3.4 29.1 - - + -
160C ASP 3.3 7.2 - - - +
161C ILE* 4.1 17.9 - - + -
162C GLU* 3.6 3.6 - - - -
187C LEU* 4.1 20.9 - - + +
188C ARG* 1.3 78.3 - - - +
190C SER* 1.3 59.9 + - - +
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Residues in contact with SER 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C PHE 5.9 0.7 - - - -
121C ASP 4.7 0.4 - - - -
122C SER* 3.3 24.7 - - - +
159C TRP* 3.4 5.6 - - - -
160C ASP* 2.8 44.5 + - - +
162C GLU* 3.2 19.2 + - - -
189C ILE* 1.3 71.0 - - - +
191C ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 2.8 34.2 + - - -
115C PHE* 4.0 7.9 - - - -
118C TYR* 3.0 31.2 - - - -
119C PRO 3.1 20.9 + - - +
120C PHE 5.0 2.0 + - - +
121C ASP* 2.6 48.7 + - - +
158C GLY 4.2 4.5 - - - +
159C TRP* 3.3 38.9 - - + +
160C ASP* 4.8 2.1 - - - +
190C SER* 1.3 78.3 + - - +
192C GLN* 1.3 75.6 + - - +
193C TYR* 3.5 19.0 + - - +
196C TYR* 4.2 20.0 + - + -
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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