Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 4LCC
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 2.8 51.2 + - - +
38A HIS 5.0 0.2 - - - -
39A ALA* 5.2 0.6 - - - +
84A ALA* 1.3 70.5 - - - +
86A TYR* 1.3 63.4 + - - +
87A LEU* 3.6 14.2 + - - +
102A GLY* 4.9 4.4 - - - -
103A THR 3.4 8.5 - - - -
104A LYS* 3.7 18.9 + - - +
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Residues in contact with TYR 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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6A GLN* 3.3 11.1 + - - -
20A ILE* 3.8 25.6 - - + -
34A TRP* 4.2 8.7 - - + -
35A TYR 3.3 4.0 - - - +
36A GLN* 3.0 26.8 + - + -
46A LEU* 3.5 24.5 - - + -
60A PHE* 5.0 2.0 - + - -
73A LEU* 3.4 18.4 - - + -
75A LEU* 3.5 27.3 - - + +
82A ASP* 2.5 34.6 + - - +
84A ALA* 3.2 21.8 - - + -
85A SER* 1.3 71.8 - - - +
87A LEU* 1.3 61.6 + - - +
102A GLY* 3.1 2.1 - - - -
103A THR 2.8 36.3 + - - -
105A LEU* 3.9 11.2 - - + -
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Residues in contact with LEU 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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33A PHE 3.7 0.9 - - - +
34A TRP* 3.4 7.4 - - - -
35A TYR* 2.7 42.8 + - + +
37A GLN* 3.7 19.1 - - + +
43A PRO* 3.4 38.6 - - + -
85A SER* 4.0 13.9 - - - +
86A TYR* 1.3 72.7 - - - +
88A CYS* 1.3 60.2 + - - +
89A ALA 4.1 0.2 + - - -
99A TRP* 3.7 28.8 - - + -
100A GLY 4.5 4.0 - - - +
102A GLY* 3.7 25.6 - - - +
37B GLN* 4.7 7.4 - - - +
43B LEU* 4.5 9.2 - - + -
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Residues in contact with CYS 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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4A ILE* 3.2 7.6 - - + +
6A GLN* 3.0 29.3 + - - +
22A CYS* 2.0 48.9 - - - -
32A LEU* 4.4 12.6 - - - -
33A PHE 3.5 5.6 - - - -
34A TRP* 3.6 17.3 - - + -
86A TYR 3.7 0.2 + - - -
87A LEU* 1.3 71.0 - - - +
89A ALA* 1.3 59.3 + - - +
99A TRP* 3.8 0.6 - - - -
100A GLY* 2.6 33.8 + - - +
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Residues in contact with ALA 89 (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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4A ILE* 4.0 0.7 - - - -
32A LEU* 4.0 0.2 - - - +
33A PHE* 2.5 48.9 + - + +
87A LEU 4.1 0.2 + - - -
88A CYS* 1.3 74.6 - - - +
90A VAL* 1.3 64.4 + - - +
97A LEU* 4.0 11.0 - - + -
98A ILE 3.3 10.1 - - - +
99A TRP* 3.4 41.1 - - + -
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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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4A ILE* 4.2 13.2 - - + +
24A TYR* 4.1 24.9 - - + -
26A THR* 4.7 8.7 - - + +
29A PHE* 3.5 22.7 - - + -
31A GLY 3.3 16.6 - - - +
32A LEU* 3.6 29.2 - - + -
33A PHE* 4.9 0.2 - - - -
89A ALA* 1.3 81.9 - - - +
91A LYS* 1.3 71.5 + - - +
97A LEU* 3.7 4.7 - - - -
98A ILE* 3.0 33.7 + - - +
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Residues in contact with LYS 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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26A THR* 4.7 0.6 + - - -
28A GLY 3.4 11.4 - - - +
30A ASN* 3.0 33.0 + - + +
31A GLY 3.7 4.2 + - - -
33A PHE* 4.0 13.7 - - + -
90A VAL* 1.3 82.1 - - - +
92A ASP* 1.3 68.8 + - - +
94A ASN 4.8 0.7 - - - +
95A TYR* 3.6 32.4 + - + +
96A GLN 3.6 4.3 - - - +
97A LEU* 3.4 22.1 - - + +
98A ILE* 5.2 0.2 - - - -
98B GLY* 3.4 23.8 - - - +
99B GLU 3.8 2.0 + - - -
100B GLY* 3.2 42.1 + - - +
102B GLY 4.8 6.5 + - - -
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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