Contacts of the strand formed by residues 99 - 108 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250G SER* 5.7 1.7 - - - -
251G ALA* 4.0 15.3 + - + +
252G ASP* 4.0 22.2 - - - +
255G LYS* 2.8 35.2 + - - +
30I ARG* 6.3 0.4 - - - -
91I SER* 5.9 4.9 - - - -
92I ILE 3.3 6.1 - - - +
93I GLN* 3.3 30.7 - - + +
97I GLY 3.5 4.8 + - - +
98I ARG* 1.3 75.9 - - - +
100I PHE* 1.3 68.5 + - - +
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Residues in contact with PHE 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255G LYS* 6.0 4.9 - - - -
91I SER* 3.3 6.8 - - - -
92I ILE* 2.8 37.7 + - + +
94I LEU* 3.7 34.5 - - + -
98I ARG* 3.6 40.8 - - + -
99I GLU* 1.3 79.1 - - - +
101I ASP* 1.3 63.1 + - - +
118I ILE* 3.5 33.7 - - + -
119I GLN 3.8 4.7 - - - -
120I ASN 3.5 22.0 - - - -
121I PRO* 4.1 1.3 - - + -
122I SER* 4.0 17.3 - - - -
124I LEU* 4.1 6.7 - - + -
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Residues in contact with ASP 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I LYS* 5.3 6.6 - - - +
90I ILE 3.3 19.0 + - - +
91I SER* 5.0 4.8 - - - -
100I PHE* 1.3 76.9 - - - +
102I ALA* 1.3 57.9 + - - +
118I ILE* 3.5 5.0 - - - -
119I GLN* 2.7 49.2 + - + -
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Residues in contact with ALA 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I ILE* 2.9 37.8 + - + +
92I ILE* 3.6 30.7 - - + -
101I ASP* 1.3 77.9 - - - +
103I LYS* 1.3 65.7 + - - +
116I LEU* 4.4 8.7 - - + -
117I GLN 3.3 14.8 - - - +
118I ILE* 4.5 3.1 - - + -
119I GLN* 4.4 1.8 - - - -
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Residues in contact with LYS 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I ILE* 5.1 0.7 - - - -
102I ALA* 1.3 77.2 - - - +
104I LEU* 1.3 67.0 + - - +
105I ILE* 3.4 6.1 + - + +
116I LEU* 3.4 5.8 - - - -
117I GLN* 2.9 32.0 + - - +
119I GLN* 3.5 38.5 + - + +
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Residues in contact with LEU 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I ILE* 3.9 26.0 - - + +
90I ILE* 4.5 10.8 - - + +
103I LYS* 1.3 74.1 - - - +
105I ILE* 1.3 62.4 + - - +
106I GLY* 3.5 29.8 - - - +
107I SER* 4.4 12.3 - - - +
114I ALA* 4.2 4.3 - - + -
115I LEU 3.6 9.0 - - - +
116I LEU* 3.8 18.5 - - + +
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Residues in contact with ILE 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I TYR* 4.3 11.2 - - + +
103I LYS* 3.4 5.8 + - + +
104I LEU* 1.3 78.7 - - - +
106I GLY* 1.3 58.6 + - - +
115I LEU* 2.8 28.4 + - + +
116I LEU 4.1 2.7 - - - -
117I GLN* 3.5 50.5 - - + +
231I LEU 3.5 23.8 - - - +
232I ILE* 4.6 4.3 - - - +
235I GLY* 3.7 15.0 - - - +
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Residues in contact with GLY 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I LEU* 3.5 10.8 - - - +
105I ILE* 1.3 82.0 - - - +
107I SER* 1.3 61.8 + - - -
115I LEU* 2.8 28.0 + - - +
231I LEU* 3.7 14.4 - - - +
235I GLY 3.8 13.9 - - - -
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Residues in contact with SER 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I ASN* 3.3 25.2 + - - -
84I ILE* 5.1 0.2 - - - -
104I LEU* 4.4 14.0 - - - +
106I GLY* 1.3 74.8 - - - -
108I ASP* 1.3 60.9 + - - +
109I ASP* 4.5 8.2 + - - +
113I ILE 3.3 10.5 - - - -
114I ALA* 4.0 9.0 - - - -
231I LEU* 3.6 14.3 - - - +
235I GLY 5.0 0.4 + - - -
236I GLU* 5.4 1.9 - - - -
237I ILE* 5.0 4.9 + - - +
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Residues in contact with ASP 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I ASN* 3.9 4.1 - - - +
107I SER* 1.3 73.2 - - - +
109I ASP* 1.3 57.1 + - - +
110I GLN* 3.2 11.3 + - - +
111I SER* 2.6 30.3 + - - +
112I ASP* 2.9 26.0 + - - -
113I ILE* 2.7 21.3 + - + +
227I LEU* 3.7 3.3 - - + +
231I LEU* 5.5 0.4 - - + -
237I ILE* 3.9 21.7 - - + +
239I ARG* 2.8 44.1 + - - -
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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