Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 3LC5
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 GLN 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.7 23.2 + - + +
19A GLY* 3.9 25.2 + - - +
20A GLU* 3.3 5.8 - - - +
21A ASP* 2.9 27.1 + - - +
139A SER* 3.3 6.1 - - - -
140A GLY 3.2 36.5 + - - +
144A VAL* 4.1 27.6 - - + +
152A ALA* 4.2 6.5 - - + -
154A VAL* 3.2 17.1 + - - +
155A LEU* 1.3 80.4 - - - +
157A TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.5 2.7 - - - -
19A GLY* 3.1 5.9 - - - -
20A GLU* 2.8 83.9 + - + +
21A ASP 3.6 18.4 - - - -
22A ALA* 3.8 13.0 - - + -
26A GLN* 3.4 24.6 + - - -
27A PHE* 3.6 31.9 - + + -
137A TYR* 4.1 24.9 - + - -
138A VAL 3.2 11.7 - - - +
139A SER* 4.1 2.7 - - - +
156A GLN* 1.3 77.3 - - - +
158A LEU* 1.3 66.3 + - - +
159A ARG* 5.3 1.1 - - + -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.8 11.9 - - + -
17A VAL 4.3 1.3 - - - +
18A GLY 3.6 20.9 - - - +
19A GLY 5.5 0.2 - - - -
20A GLU* 5.6 3.4 - - - +
136A GLY 3.7 0.3 - - - +
137A TYR* 3.4 2.5 - - - -
138A VAL* 2.6 44.0 + - + +
157A TYR* 1.3 82.7 - - - +
159A ARG* 1.3 63.6 + - - +
160A VAL* 3.4 26.4 + - + -
184A PHE* 4.1 5.6 - - + +
188A ARG* 3.8 35.0 - - + +
189A ASP* 3.5 38.8 - - - +
190A SER 4.5 0.4 - - - +
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 5.8 0.8 + - - -
135A SER* 3.1 32.2 + - - +
136A GLY 3.4 7.6 - - - +
137A TYR* 3.5 49.0 + - + +
157A TYR* 4.9 2.5 - - + -
158A LEU* 1.3 76.1 - - - +
160A VAL* 1.3 59.6 + - - +
161A PRO* 4.1 0.7 - - - +
184A PHE* 3.5 19.1 + - - -
188A ARG* 5.2 1.4 + - - -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 3.4 4.0 - - - -
136A GLY 2.8 41.7 + - - +
138A VAL* 3.8 22.7 - - + -
158A LEU* 3.4 35.9 - - + +
159A ARG* 1.3 71.5 - - - +
161A PRO* 1.3 68.6 - - + +
162A LEU 3.8 0.2 + - - -
183A ALA* 3.7 24.2 - - + -
184A PHE* 4.2 13.9 - - + +
188A ARG 5.4 0.7 - - - +
189A ASP* 5.4 3.1 - - - +
190A SER 5.5 0.2 - - - +
199A HIS* 4.0 9.2 + - + -
228A TYR* 4.3 11.0 - - - +
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Residues in contact with PRO 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLY 3.2 10.5 - - - +
135A SER* 4.5 1.8 - - - +
159A ARG 4.2 0.9 - - - +
160A VAL* 1.3 85.4 - - + +
162A LEU* 1.3 68.9 + - - +
163A VAL* 3.3 0.6 + - + -
183A ALA* 3.3 3.9 - - - -
184A GLY* 3.0 80.7 + - + +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.9 43.5 - - + +
132A LYS* 4.8 23.1 - - + +
134A GLY* 2.7 29.0 + - - +
160A VAL 3.8 1.0 + - - -
161A PRO* 1.3 74.5 - - - +
163A VAL* 1.3 71.7 + - - +
164A ASP* 4.0 2.8 + - - +
181A PHE* 3.9 22.2 - - + -
182A CYS 4.0 6.3 - - - +
183A ALA* 4.5 3.1 - - - -
199A HIS* 6.1 0.4 + - - -
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PRO 3.3 0.2 + - - -
162A LEU* 1.3 85.9 - - - +
164A ASP* 1.3 76.7 + - - +
165A ARG* 3.8 0.7 + - - -
167A THR* 4.0 13.5 - - + -
168A CYS* 4.3 4.7 - - + +
181A PHE* 5.9 0.2 - - - +
182A CYS* 3.0 26.0 + - + +
183A ALA* 3.9 2.7 - - - -
184A GLY 3.5 27.6 - - - +
185A HIS* 4.4 10.1 - - + -
225A TYR* 3.5 51.8 - - + -
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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