Contacts of the strand formed by residues 99 - 108 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A SER* 5.6 1.4 - - - -
251A ALA* 3.8 26.0 + - + +
252A ASP* 4.2 16.9 - - - +
255A LYS* 3.0 33.0 + - - +
30C ARG* 5.6 6.1 + - - -
91C SER* 5.9 5.4 - - - -
92C ILE 3.3 6.5 - - - +
93C GLN* 3.3 29.1 - - + +
97C GLY 3.5 5.1 + - - +
98C ARG* 1.3 75.8 - - - +
100C PHE* 1.3 68.9 + - - +
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Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER* 3.3 7.0 - - - -
92C ILE* 2.8 37.6 + - + +
94C LEU* 3.7 33.9 - - + -
98C ARG* 3.5 39.9 - - + -
99C GLU* 1.3 79.0 - - - +
101C ASP* 1.3 62.9 + - - +
118C ILE* 3.5 34.3 - - + -
119C GLN 3.8 5.2 - - - -
120C ASN 3.5 22.7 - - - -
121C PRO* 4.1 1.3 - - + -
122C SER* 3.9 17.0 - - - -
124C LEU* 4.0 6.5 - - + -
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Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C LYS* 5.4 5.7 - - - +
90C ILE 3.3 18.6 + - - +
91C SER* 5.0 4.7 - - - -
100C PHE* 1.3 76.6 - - - +
102C ALA* 1.3 62.6 + - - +
118C ILE* 3.5 5.0 - - - -
119C GLN* 2.8 44.8 + - + -
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ILE* 2.9 38.8 + - + +
92C ILE* 3.6 31.6 - - + -
101C ASP* 1.3 77.8 - - - +
103C LYS* 1.3 67.5 + - - +
116C LEU* 4.4 8.1 - - + -
117C GLN 3.2 14.8 - - - +
118C ILE* 4.5 2.9 - - + -
119C GLN* 4.4 0.9 - - - -
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Residues in contact with LYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ILE* 5.0 0.9 - - - -
102C ALA* 1.3 77.5 - - - +
104C LEU* 1.3 64.8 + - - +
105C ILE* 3.4 6.4 + - + +
116C LEU* 3.4 5.8 - - - -
117C GLN* 2.9 32.1 + - - +
119C GLN* 3.6 38.4 + - + +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ILE* 3.9 25.4 - - + +
90C ILE* 4.5 12.7 - - + +
103C LYS* 1.3 72.4 - - - +
105C ILE* 1.3 63.1 + - - +
106C GLY* 3.4 30.7 - - - +
107C SER* 4.4 11.9 - - - +
114C ALA* 4.2 4.3 - - + -
115C LEU 3.5 8.5 - - - +
116C LEU* 3.8 18.8 - - + +
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Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C TYR* 4.3 11.0 - - + -
103C LYS* 4.3 6.3 - - + +
104C LEU* 1.3 78.1 - - - +
106C GLY* 1.3 60.1 + - - +
115C LEU* 2.8 31.1 + - + +
116C LEU 4.1 2.5 - - - -
117C GLN* 3.4 49.4 - - + +
231C LEU 3.5 24.2 - - - +
232C ILE* 4.6 4.3 - - - +
235C GLY* 3.8 14.6 - - - +
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Residues in contact with GLY 106 (chain C).
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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104C LEU* 3.4 12.5 - - - +
105C ILE* 1.3 81.5 - - - +
107C SER* 1.3 60.4 + - - -
115C LEU* 2.8 28.8 + - - +
231C LEU* 3.7 20.0 - - - +
235C GLY 3.9 8.3 - - - -
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ASN* 3.3 25.4 + - - -
84C ILE* 5.1 0.2 - - - -
104C LEU* 4.4 13.8 - - - +
106C GLY* 1.3 74.2 - - - -
108C ASP* 1.3 59.7 + - - +
109C ASP* 4.2 8.5 + - - +
113C ILE 3.3 11.0 - - - -
114C ALA* 4.0 9.2 - - - +
231C LEU* 3.5 15.3 - - - +
235C GLY 5.0 0.2 + - - -
236C GLU* 5.4 1.9 - - - -
237C ILE* 5.0 5.5 + - - +
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Residues in contact with ASP 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ASN* 3.9 4.4 - - - +
107C SER* 1.3 73.6 - - - +
109C ASP* 1.3 59.2 + - - +
110C GLN* 3.2 11.4 + - - +
111C SER* 2.6 29.6 + - - +
112C ASP* 3.0 23.0 + - - -
113C ILE* 2.7 20.6 + - + +
227C LEU* 3.7 4.2 - - + +
231C LEU* 5.6 0.4 - - + -
237C ILE* 3.9 24.3 - - + +
239C ARG* 2.9 44.5 + - - -
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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