Contacts of the strand formed by residues 99 - 108 (chain L) in PDB entry 3STJ
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 GLU 99 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250J SER* 5.8 1.2 - - - -
251J ALA* 3.9 21.8 + - + +
252J ASP* 3.7 20.5 - - - +
255J LYS* 3.1 29.1 + - - +
30L ARG* 6.3 0.9 - - - -
91L SER* 5.9 5.4 - - - -
92L ILE 3.3 7.2 - - - +
93L GLN* 3.3 28.7 - - + +
97L GLY 3.5 7.4 + - - +
98L ARG* 1.3 76.0 - - - +
100L PHE* 1.3 68.3 + - - +
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Residues in contact with PHE 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255J LYS* 5.0 5.8 - - - +
91L SER* 3.3 7.0 - - - -
92L ILE* 2.8 38.6 + - + +
94L LEU* 3.7 34.5 - - + -
98L ARG* 3.5 39.9 - - + -
99L GLU* 1.3 78.5 - - - +
101L ASP* 1.3 63.7 + - - +
118L ILE* 3.5 32.5 - - + -
119L GLN 3.8 4.5 - - - +
120L ASN 3.5 22.2 - - - -
121L PRO* 4.1 1.3 - - + -
122L SER* 3.9 17.3 - - - -
124L LEU* 4.0 6.3 - - + -
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Residues in contact with ASP 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L LYS* 5.4 6.1 - - - +
90L ILE 3.3 19.0 + - - +
91L SER* 5.1 4.8 - - - -
100L PHE* 1.3 76.5 - - - +
102L ALA* 1.3 60.3 + - - +
118L ILE* 3.5 4.9 - - - -
119L GLN* 2.8 44.4 + - + -
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Residues in contact with ALA 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L ILE* 2.9 38.3 + - + +
92L ILE* 3.6 31.2 - - + -
101L ASP* 1.3 78.4 - - - +
103L LYS* 1.3 67.4 + - - +
116L LEU* 4.4 8.5 - - + -
117L GLN 3.3 14.6 - - - +
118L ILE* 4.5 2.7 - - + -
119L GLN* 4.4 1.6 - - - -
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Residues in contact with LYS 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L ILE* 5.0 0.7 - - - -
102L ALA* 1.3 78.1 - - - +
104L LEU* 1.3 65.2 + - - +
105L ILE* 3.4 6.6 + - + +
116L LEU* 3.4 5.1 - - - -
117L GLN* 2.8 32.5 + - - +
119L GLN* 3.5 39.1 + - + +
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Residues in contact with LEU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L ILE* 3.9 26.2 - - + +
90L ILE* 4.4 12.7 - - + +
103L LYS* 1.3 73.3 - - - +
105L ILE* 1.3 61.4 + - - +
106L GLY* 3.4 30.3 - - - +
107L SER* 4.4 11.4 - - - +
114L ALA* 4.1 4.9 - - + -
115L LEU 3.5 9.2 - - - +
116L LEU* 3.8 19.4 - - + +
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Residues in contact with ILE 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L TYR* 4.2 12.1 - - + +
103L LYS* 3.4 6.3 + - + +
104L LEU* 1.3 77.1 - - - +
106L GLY* 1.3 60.0 + - - +
115L LEU* 2.8 29.5 + - + +
116L LEU 4.1 3.1 - - - -
117L GLN* 3.5 50.5 - - + +
231L LEU 3.5 23.1 - - - +
232L ILE* 4.6 4.5 - - - +
235L GLY* 3.8 15.4 - - - +
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Residues in contact with GLY 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L LEU* 3.4 11.1 - - - +
105L ILE* 1.3 82.4 - - - +
107L SER* 1.3 61.7 + - - -
115L LEU* 2.8 28.9 + - - +
231L LEU* 3.6 13.8 - - - +
235L GLY 3.9 14.4 - - - -
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Residues in contact with SER 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L ASN* 3.3 25.5 + - - -
84L ILE* 5.1 0.4 - - - -
104L LEU* 4.4 14.2 - - - +
106L GLY* 1.3 74.7 - - - -
108L ASP* 1.3 60.3 + - - +
109L ASP* 4.2 8.4 + - - +
113L ILE 3.3 10.5 - - - -
114L ALA* 3.8 9.4 - - - -
231L LEU* 3.7 15.6 - - - +
235L GLY 4.9 0.6 + - - -
236L GLU* 5.3 2.3 - - - +
237L ILE* 5.0 4.0 + - - +
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Residues in contact with ASP 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L ASN* 3.9 4.0 - - - +
107L SER* 1.3 73.2 - - - +
109L ASP* 1.3 58.8 + - - +
110L GLN* 3.2 11.1 + - - +
111L SER* 2.6 28.7 + - - +
112L ASP* 2.9 26.3 + - - -
113L ILE* 2.7 21.3 + - + +
227L LEU* 3.8 3.7 - - + +
231L LEU* 5.5 0.2 - - + -
237L ILE* 3.8 22.8 - - + +
239L ARG* 2.8 44.8 + - - -
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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