Contacts of the strand formed by residues 71 - 78 (chain A) in PDB entry 1LEC
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 SER 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ALA 3.7 1.4 + - - -
70A ALA* 1.3 76.7 - - - +
72A PHE* 1.3 60.4 + - - +
178A TYR 3.3 12.1 + - - -
179A ASP* 3.7 4.0 - - - -
180A ALA* 3.0 25.5 + - - +
181A ARG* 3.8 19.9 + - - -
236A SER* 3.1 3.8 - - - -
237A THR* 2.8 50.2 + - - -
239A ASP 4.7 1.9 + - - -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.5 9.6 - - + -
70A ALA* 4.5 4.7 - - + -
71A SER* 1.3 76.4 - - - +
73A TYR* 1.3 71.1 + - - +
74A THR* 4.5 1.3 - - + -
93A PHE* 4.7 8.7 - + - -
95A LEU* 4.0 31.9 - - + -
176A ILE* 4.4 20.4 - - + -
177A THR* 3.3 2.9 - - - -
178A TYR* 2.9 66.8 + + + +
185A LEU* 4.3 8.3 - - + -
205A LEU* 3.8 17.7 - - + -
234A PHE* 3.6 33.4 - + + -
235A PHE* 3.2 14.4 - - - +
236A SER* 4.0 3.4 - - - -
237A THR* 5.6 0.2 - - - -
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Residues in contact with TYR 73 (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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72A PHE* 1.3 81.6 - - - +
74A THR* 1.3 77.1 + - - +
75A SER* 3.5 12.3 + - - -
175A HIS* 2.6 47.0 + - + -
176A ILE 3.3 12.3 - - - -
177A THR* 3.5 19.5 - - + -
233A HIS* 3.8 24.4 - + - +
234A PHE* 3.4 2.6 - - - -
235A PHE* 2.8 49.3 + + + +
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Residues in contact with THR 74 (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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72A PHE* 4.5 2.2 - - + -
73A TYR* 1.3 79.2 - - - +
75A SER* 1.3 57.7 + - - +
76A PHE* 4.3 6.1 - - + -
93A PHE* 3.9 26.7 - - + -
174A ALA 3.8 0.5 - - - +
175A HIS* 3.5 2.6 - - - -
176A ILE* 2.9 60.0 + - + +
232A TRP* 3.0 21.1 + - - -
233A HIS 2.7 17.2 + - - -
234A PHE* 3.7 18.3 - - - -
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Residues in contact with SER 75 (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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73A TYR* 3.5 24.0 + - - -
74A THR* 1.3 75.3 - - - +
76A PHE* 1.3 65.1 + - - +
173A THR* 5.2 3.6 - - - -
174A ALA 3.1 11.2 - - - -
175A HIS* 3.7 10.8 - - - -
232A TRP* 3.6 2.3 - - - -
233A HIS* 2.8 51.3 + - - +
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Residues in contact with PHE 76 (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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74A THR* 4.3 9.9 - - + -
75A SER* 1.3 80.2 - - - +
77A THR* 1.3 63.9 + - - +
78A PHE* 3.5 37.1 + + + -
91A LEU* 4.6 4.9 - - + -
93A PHE* 4.2 8.3 - + + -
130A PHE* 4.1 19.3 - + - -
172A ALA 3.9 0.3 - - - +
173A THR* 3.5 2.6 - - - +
174A ALA* 2.8 49.0 + - + -
176A ILE* 3.7 24.2 - - + -
217A PHE* 3.5 44.9 - + + -
229A ILE* 4.5 2.0 - - + -
231A SER* 3.3 20.2 - - - +
232A TRP* 4.1 1.6 - + + -
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Residues in contact with THR 77 (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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76A PHE* 1.3 77.9 - - - +
78A PHE* 1.3 64.7 + - - +
171A ILE* 4.1 14.4 - - + -
172A ALA 3.1 8.1 - - - -
173A THR* 3.5 27.6 - - + +
229A ILE* 3.7 6.2 - - - +
230A LEU* 2.8 39.6 + - - +
231A SER* 2.8 27.4 + - - +
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Residues in contact with PHE 78 (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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76A PHE* 3.5 31.0 - + + -
77A THR* 1.3 78.0 - - - +
79A LEU* 1.3 61.8 + - - +
80A LEU* 4.0 18.6 - - + -
91A LEU* 4.1 26.2 - - + -
130A PHE* 4.5 18.6 - + - -
161A TRP* 5.0 9.0 - + - -
170A SER 4.0 1.5 - - - +
171A ILE* 3.4 3.1 - - - -
172A ALA* 3.0 53.9 + - + -
174A ALA* 4.5 3.6 - - + -
189A LEU* 4.0 26.0 - - + -
191A TYR* 5.0 2.5 - - - -
227A THR* 4.4 2.0 - - + -
228A TYR 3.3 12.6 - - - +
229A ILE* 3.8 15.7 - - + -
230A LEU* 4.3 6.3 - - - +
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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