Contacts of the strand formed by residues 82 - 91 (chain A) in PDB entry 1LCY
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 THR 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 4.0 27.9 + - - +
75A VAL 3.1 5.8 - - - -
76A ARG* 3.6 35.0 - - + +
80A GLY 3.5 4.5 + - - +
81A ASP* 1.3 76.5 - - - +
83A TYR* 1.3 72.0 + - - +
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Residues in contact with TYR 83 (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 ARG* 3.4 9.2 - - - +
75A VAL* 2.7 37.9 + - + +
77A LEU* 3.7 30.4 - - + +
81A ASP* 3.9 27.2 + - + +
82A THR* 1.3 81.7 - - - +
84A GLU* 1.3 62.3 + - - +
101A ILE* 4.1 27.6 - - + -
102A GLN 3.5 27.1 - - - +
103A THR* 3.7 29.4 - - + +
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Residues in contact with GLU 84 (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 ARG* 3.5 47.2 + - - +
73A VAL 2.9 29.6 - - - +
74A ARG* 4.6 2.4 - - - +
83A TYR* 1.3 74.7 - - - +
85A ALA* 1.3 61.8 + - - +
86A VAL* 5.4 1.0 - - - +
100A ARG 4.2 2.6 - - - +
101A ILE* 4.2 9.5 - - - +
102A GLN 5.1 1.7 + - - -
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Residues in contact with ALA 85 (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 ARG* 3.1 11.7 - - - +
73A VAL* 2.9 38.3 + - + +
75A VAL* 3.8 6.5 - - + -
83A TYR 3.6 0.6 + - - -
84A GLU* 1.3 73.5 + - - +
86A VAL* 1.3 63.1 + - - +
99A LEU* 3.5 27.4 - - + -
100A ARG 3.4 6.7 - - - +
101A ILE* 3.4 22.9 - - + -
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Residues in contact with VAL 86 (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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71A ARG* 3.6 25.1 - - - +
72A ARG* 3.1 37.7 - - + +
84A GLU 5.4 0.9 - - - +
85A ALA* 1.3 72.9 - - - +
87A VAL* 1.3 74.4 + - - +
88A THR* 3.4 10.2 + - + +
99A LEU* 3.0 4.1 - - - -
100A ARG* 2.8 36.4 + - + +
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Residues in contact with VAL 87 (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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67A VAL* 4.0 30.7 - - + -
70A ARG 3.5 24.2 - - - +
71A ARG* 3.0 25.3 + - - +
72A ARG* 4.8 0.4 - - - -
73A VAL* 4.2 11.4 - - + -
86A VAL* 1.3 80.4 - - - +
88A THR* 1.3 61.3 + - - +
89A ALA 4.1 1.8 - - - +
90A VAL* 3.6 31.2 - - + -
97A ALA* 4.7 0.9 - - + -
98A THR 3.6 12.3 - - - +
99A LEU* 4.0 5.8 - - + -
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Residues in contact with THR 88 (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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59A LEU* 4.5 2.9 - - - +
86A VAL* 3.6 21.8 - - + +
87A VAL* 1.3 74.8 - - - +
89A ALA* 1.3 57.5 + - - +
98A THR* 2.7 39.9 + - - -
99A LEU 3.9 0.3 + - - -
100A ARG* 3.7 32.1 - - + +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.8 1.8 - - - +
88A THR* 1.3 83.3 + - - +
90A VAL* 1.3 68.8 + - - +
97A ALA* 3.1 3.3 - - - +
98A THR* 2.8 39.7 + - + +
208A PHE* 3.6 18.6 - - + -
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Residues in contact with VAL 90 (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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64A ALA* 3.6 26.7 - - + +
67A VAL* 4.3 7.4 - - + -
68A ALA 5.3 7.0 - - - +
87A VAL* 3.6 22.2 - - + -
89A ALA* 1.3 82.6 - - - +
91A ASP* 1.3 65.2 + - - +
92A PRO* 3.6 21.8 - - + +
96A ILE 3.6 3.8 - - - -
97A ALA* 3.8 6.7 - - + -
208A PHE* 4.2 5.1 - - - -
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Residues in contact with ASP 91 (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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90A VAL* 1.3 75.4 - - - +
92A PRO* 1.3 58.4 - - - +
93A VAL* 3.2 26.2 + - - +
94A ALA* 3.8 18.1 - - - +
95A ASP 2.9 23.4 + - - -
96A ILE* 2.8 26.4 + - + +
204A ARG* 4.4 9.9 + - - -
208A PHE* 3.7 26.3 - - + +
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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