Contacts of the strand formed by residues 177 - 184 (chain A) in PDB entry 1LA5
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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ASP* 3.1 29.4 + - - -
81A VAL* 4.7 7.8 - - + +
82A ASN* 5.8 0.4 - - - -
171A LEU 3.0 20.9 - - - -
172A THR 4.0 2.9 + - - -
174A GLN* 2.9 27.8 - - + -
175A GLY* 2.8 51.1 + - - -
176A ASN* 1.4 82.7 + - - +
178A GLU* 1.3 57.7 + - - +
197A THR* 3.3 6.2 + - - -
198A PHE 2.8 36.0 + - - +
298A LEU* 3.0 37.0 - - + -
299A ARG* 2.9 39.2 + - - +
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Residues in contact with GLU 178 (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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130A TRP* 4.0 5.1 - - + -
176A ASN* 4.9 2.1 - - - +
177A TRP* 1.3 77.5 - - - +
179A LEU* 1.3 57.7 + - - +
194A HIS* 2.8 44.0 + - + +
195A TYR 3.2 10.8 - - - +
196A ALA* 3.9 10.3 - - + +
197A THR 5.3 0.3 + - - -
198A PHE 4.5 0.2 - - - +
298A LEU* 2.7 17.6 - - - +
299A ARG* 2.7 62.8 + - - +
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Residues in contact with LEU 179 (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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130A TRP* 4.6 0.9 - - - -
133A PHE* 4.5 13.5 - - + -
178A GLU* 1.3 75.0 - - - +
180A ARG* 1.3 60.5 + - - +
181A VAL* 4.2 15.0 - - + -
194A HIS* 3.5 4.4 - - - -
195A TYR* 2.8 59.8 + - + -
198A PHE* 2.9 54.2 - - + +
211A LEU* 3.5 11.0 - - + -
223A LEU* 3.8 11.4 - - + -
296A MET* 5.8 3.8 - - + -
297A MET 3.3 8.5 - - - +
298A LEU* 4.1 1.8 - - + -
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Residues in contact with ARG 180 (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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125A THR* 3.5 22.0 - - - +
126A GLU* 3.0 28.7 + - - +
130A TRP* 3.5 39.4 - - + -
179A LEU* 1.3 74.8 - - - +
181A VAL* 1.3 70.3 + - - +
182A GLU* 2.7 40.0 + - + +
190A ARG* 4.8 6.9 - - - +
192A PHE* 3.7 37.0 - - + +
193A ALA 3.4 9.6 - - - +
194A HIS* 4.6 7.4 - - + +
216A GLU* 4.8 2.6 + - - -
295A ARG 3.7 0.7 - - - +
296A MET* 3.7 4.0 - - - -
297A MET* 2.8 36.8 + - + +
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Residues in contact with VAL 181 (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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179A LEU* 4.2 17.9 - - + -
180A ARG* 1.3 77.8 - - - +
182A GLU* 1.3 60.4 + - - +
183A LEU* 3.1 36.3 - - + -
192A PHE* 3.0 28.8 - - - +
193A ALA* 2.9 19.1 + - + +
195A TYR* 4.9 0.9 - - + -
223A LEU* 5.4 2.5 - - + -
263A LEU* 4.2 7.4 - - + -
281A TRP* 4.1 30.5 - - + -
295A ARG 3.5 7.6 - - - +
296A MET* 4.4 15.9 - - + -
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Residues in contact with GLU 182 (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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125A THR* 4.6 8.7 + - - +
180A ARG* 2.7 48.6 + - + +
181A VAL* 1.3 72.4 - - - +
183A LEU* 1.4 61.9 + - - +
190A ARG* 2.9 31.0 + - - -
191A THR 3.9 0.4 - - - -
192A PHE* 3.2 13.5 - - - +
293A ARG 4.2 0.2 - - - +
294A VAL* 3.3 6.1 - - - -
295A ARG* 3.0 68.2 + - + +
297A MET* 4.3 14.1 - - + -
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Residues in contact with LEU 183 (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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181A VAL* 3.1 28.9 - - + -
182A GLU* 1.4 77.8 - - - +
184A GLU* 1.4 60.2 + - - +
190A ARG* 2.7 26.7 - - - +
191A THR* 2.9 42.9 + - + +
219A ALA* 4.4 1.8 - - + -
263A LEU* 4.6 5.2 - - + -
279A ILE* 6.0 0.2 - - + -
281A TRP* 3.4 50.0 - - + -
291A TYR* 4.7 16.6 - - + +
293A ARG 3.9 1.8 - - - -
294A VAL* 3.4 24.9 - - + -
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Residues in contact with GLU 184 (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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183A LEU* 1.4 81.4 - - - +
185A ASP* 1.4 64.9 + - - +
188A GLY* 4.0 15.4 - - - +
189A ASN 3.3 7.4 - - - +
190A ARG* 3.6 24.6 + - + +
291A TYR* 3.8 9.4 - - - +
292A ARG* 3.6 7.2 + - + +
293A ARG* 3.1 69.7 + - + +
295A ARG* 3.7 22.2 + - - +
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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