Contacts of the strand formed by residues 99 - 108 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30K ARG* 6.0 1.5 + - - -
91K SER* 5.8 6.1 - - - -
92K ILE 3.3 7.0 - - - +
93K GLN* 3.3 28.7 - - + +
97K GLY 3.5 8.3 + - - +
98K ARG* 1.3 75.1 - - - +
100K PHE* 1.3 67.7 + - - +
250L SER* 5.4 2.3 - - - -
251L ALA* 3.9 23.2 + - + +
252L ASP* 3.9 24.3 - - - +
255L LYS* 2.7 31.0 + - - +
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Residues in contact with PHE 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K SER* 3.3 6.7 - - - -
92K ILE* 2.8 37.5 + - + +
94K LEU* 3.7 34.8 - - + -
98K ARG* 3.5 39.9 - - + -
99K GLU* 1.3 79.0 - - - +
101K ASP* 1.3 62.9 + - - +
118K ILE* 3.5 33.7 - - + -
119K GLN 3.8 4.5 - - - -
120K ASN 3.5 23.6 - - - -
121K PRO* 4.1 1.6 - - + -
122K SER* 4.0 16.4 - - - -
124K LEU* 4.0 7.2 - - + -
255L LYS* 6.1 3.4 - - - -
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Residues in contact with ASP 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K LYS* 5.4 6.1 - - - +
90K ILE 3.3 18.4 + - - +
91K SER* 5.1 5.2 - - - -
100K PHE* 1.3 78.5 - - - +
102K ALA* 1.3 60.6 + - - +
118K ILE* 3.5 5.2 - - - -
119K GLN* 2.8 43.5 + - + -
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Residues in contact with ALA 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K ILE* 2.9 38.5 + - + +
92K ILE* 3.6 31.6 - - + -
101K ASP* 1.3 78.0 - - - +
103K LYS* 1.3 65.2 + - - +
116K LEU* 4.3 10.8 - - + -
117K GLN 3.3 13.0 - - - +
118K ILE* 4.5 2.5 - - + -
119K GLN* 4.4 0.9 - - - -
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Residues in contact with LYS 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K ILE* 5.0 0.4 - - - -
102K ALA* 1.3 77.4 - - - +
104K LEU* 1.3 65.3 + - - +
105K ILE* 3.3 6.9 + - + +
116K LEU* 3.4 4.8 - - - -
117K GLN* 2.9 32.1 + - - +
119K GLN* 3.5 40.0 + - + +
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Residues in contact with LEU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K ILE* 4.0 25.6 - - + +
90K ILE* 4.5 12.9 - - + +
103K LYS* 1.3 72.8 - - - +
105K ILE* 1.3 63.1 + - - +
106K GLY* 3.5 30.1 - - - +
107K SER* 4.4 12.6 - - - +
114K ALA* 4.1 4.3 - - + -
115K LEU 3.5 9.2 - - - +
116K LEU* 3.8 19.4 - - + +
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Residues in contact with ILE 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K TYR* 4.3 12.1 - - + +
103K LYS* 3.3 8.5 + - + +
104K LEU* 1.3 75.2 - - - +
106K GLY* 1.3 59.0 + - - +
115K LEU* 2.8 29.3 + - + +
116K LEU 4.1 2.7 - - - -
117K GLN* 3.5 49.6 - - + +
231K LEU 3.3 24.2 - - - +
232K ILE* 4.6 4.7 - - - +
235K GLY* 3.6 14.8 - - - +
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Residues in contact with GLY 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K LEU* 3.5 10.9 - - - +
105K ILE* 1.3 82.2 - - - +
107K SER* 1.3 59.5 + - - -
115K LEU* 2.8 30.6 + - - +
231K LEU* 3.5 13.1 - - - +
235K GLY 3.5 15.3 - - - -
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Residues in contact with SER 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K ASN* 3.3 25.1 + - - -
84K ILE* 5.0 0.2 - - - -
104K LEU* 4.4 13.7 - - - +
106K GLY* 1.3 75.0 - - - -
108K ASP* 1.4 58.5 + - - +
109K ASP* 4.2 8.4 + - - +
113K ILE 3.3 10.3 - - - -
114K ALA* 4.0 9.2 - - - +
231K LEU* 3.7 11.4 - - - +
235K GLY 4.7 0.8 + - - -
236K GLU* 5.3 1.6 - - - -
237K ILE* 3.6 15.2 - - - +
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Residues in contact with ASP 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K ASN* 3.9 4.5 - - - +
107K SER* 1.4 73.0 - - - +
109K ASP* 1.3 58.2 + - - +
110K GLN* 3.2 10.4 + - - +
111K SER* 2.6 30.7 + - - +
112K ASP* 3.0 25.8 + - - -
113K ILE* 2.7 20.8 + - + +
227K LEU* 3.7 3.9 - - + +
231K LEU* 5.6 0.4 - - + -
237K ILE* 3.9 26.9 - - + +
239K ARG* 2.8 45.1 + - - -
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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