Contacts of the strand formed by residues 90 - 98 (chain T) in PDB entry 3L9J
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 LYS 90 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47T GLN* 5.2 1.8 - - - +
81T SER* 3.9 26.5 - - - +
82T ARG 3.3 3.4 - - - -
83T ILE* 3.9 24.5 - - + +
88T GLN 3.5 4.2 + - - +
89T THR* 1.3 73.2 - - - +
91T VAL* 1.3 66.4 + - - +
92T ASN* 5.0 5.1 + - - +
133T SER* 4.0 3.6 + - - -
135T GLU* 2.6 36.8 + - - -
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Residues in contact with VAL 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T SER* 3.2 1.7 - - - -
82T ARG* 2.8 44.5 + - + +
89T THR* 4.8 10.5 - - - +
90T LYS* 1.3 83.5 - - - +
92T ASN* 1.3 67.6 + - - +
93T LEU* 3.5 19.7 + - + -
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Residues in contact with ASN 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79T THR* 3.3 24.8 + - + +
80T ILE 3.8 3.1 - - - -
81T SER* 2.6 27.9 + - - -
90T LYS* 5.0 6.5 + - - +
91T VAL* 1.3 78.4 - - - +
93T LEU* 1.3 64.9 + - - +
94T LEU 4.8 1.6 - - - +
95T SER* 4.7 11.6 + - - -
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Residues in contact with LEU 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T ILE* 3.5 26.9 - - + -
80T ILE* 2.8 10.7 + - + +
81T SER 4.6 1.1 - - - -
82T ARG* 3.8 44.2 - - + +
91T VAL* 3.5 14.3 + - + -
92T ASN* 1.3 76.2 - - - +
94T LEU* 1.3 64.6 + - + +
124T PHE* 3.5 50.8 - - + -
126T LEU* 4.4 6.7 - - + -
132T LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T ILE* 3.6 39.7 - - + +
79T THR* 3.3 1.7 - - - +
80T ILE* 2.8 47.7 + - + +
92T ASN 3.7 0.2 - - - -
93T LEU* 1.3 87.1 - - + +
95T SER* 1.3 63.9 + - - +
120T LEU* 3.9 17.0 - - + -
121T GLY 3.8 28.5 - - - +
122T GLY* 3.8 2.9 - - - +
124T PHE* 3.7 18.4 - - + -
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Residues in contact with SER 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77T THR* 5.6 0.9 - - - -
78T HIS 3.4 5.6 + - - -
79T THR* 2.9 26.5 + - - +
92T ASN* 4.7 10.9 + - - -
94T LEU* 1.3 77.0 - - - +
96T ALA* 1.3 68.9 + - - +
97T ILE* 5.3 3.3 - - - +
120T LEU* 3.8 7.2 - - - +
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Residues in contact with ALA 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77T THR* 3.4 3.5 - - - -
78T HIS 2.9 31.7 + - - +
95T SER* 1.3 80.0 + - - +
97T ILE* 1.3 68.1 + - - +
118T ILE* 3.7 29.3 - - + +
119T TYR 5.5 0.9 - - - +
120T LEU* 3.9 7.4 - - + +
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Residues in contact with ILE 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75T LEU* 4.4 21.5 - - + -
76T LEU 3.2 11.7 - - - +
77T THR* 4.1 19.5 - - + -
95T SER* 5.3 4.0 - - - +
96T ALA* 1.3 85.3 - - - +
98T LYS* 1.3 77.3 + - - +
118T ILE* 4.4 1.3 - - - -
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Residues in contact with LYS 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75T LEU* 3.4 4.6 - - - -
76T LEU* 2.7 49.7 + - + +
97T ILE* 1.3 82.5 - - - +
99T SER* 1.3 60.9 + - - +
100T PRO* 3.6 2.4 - - - +
116T GLU* 2.6 37.9 + - + +
117T PRO* 2.8 40.1 + - - +
118T ILE* 3.8 20.6 - - + +
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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