Contacts of the strand formed by residues 92 - 98 (chain K) in PDB entry 3J0O
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 ALA 92 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26K ASN* 4.8 7.6 - - + +
27K VAL 2.9 21.5 + - - +
28K PHE* 3.3 23.6 - - + -
29K GLY 2.8 23.0 + - - -
90K ILE* 3.4 1.4 - - - +
91K ASN* 1.3 83.9 - - - +
93K LEU* 1.3 68.1 + - - +
125K LYS* 3.2 18.4 - - + +
126K ILE 5.5 0.4 - - - -
127K GLY 5.0 0.4 - - - +
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Residues in contact with LEU 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K PHE* 4.6 0.4 - - - -
29K GLY* 2.9 33.2 - - - +
31K CYS* 4.4 16.8 - - + -
44K VAL* 4.2 22.2 - - + -
81K VAL* 5.5 3.4 - - + -
82K VAL* 6.0 0.9 - - + -
85K CYS* 4.5 8.3 - - - -
90K ILE* 4.1 9.6 - - + -
92K ALA* 1.3 83.9 - - - +
94K HIS* 1.3 64.2 + - - +
95K ILE* 3.9 2.4 - - + +
119K LEU* 4.8 15.3 - - + -
124K MET* 3.8 31.4 - - + -
125K LYS 2.8 12.7 + - - +
126K ILE* 3.5 11.9 - - + +
127K GLY 2.7 27.0 + - - +
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Residues in contact with HIS 94 (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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28K PHE* 3.4 51.7 - + + -
29K GLY 2.7 5.5 + - - -
30K VAL* 3.4 32.5 - - + -
31K CYS* 2.5 35.0 + - - +
47K LEU* 4.7 9.8 - - + +
93K LEU* 1.3 73.8 - - - +
95K ILE* 1.3 58.6 + - - +
96K LYS* 4.9 11.2 - - - +
127K GLY* 3.6 2.6 - - - -
128K ARG* 3.2 52.1 + - + +
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Residues in contact with ILE 95 (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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31K CYS* 3.3 15.3 - - + +
33K ILE* 4.1 24.5 - - + -
93K LEU* 3.9 2.7 - - + +
94K HIS* 1.3 77.0 - - - +
96K LYS* 1.3 69.9 + - - +
97K LEU* 3.8 5.6 - - + +
116K LEU* 4.4 23.6 - - + -
119K LEU* 5.9 2.2 - - + -
126K ILE* 3.2 35.4 - - + -
128K ARG 3.1 8.2 + - - +
129K ILE* 3.2 30.6 - - + -
130K GLU 2.9 27.5 + - - -
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Residues in contact with LYS 96 (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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30K VAL* 3.9 36.6 - - + -
31K CYS 2.9 6.8 + - - +
32K HIS* 3.3 20.2 - - + +
33K ILE 2.9 25.1 + - - +
94K HIS* 4.9 9.2 - - - +
95K ILE* 1.3 81.0 + - - +
97K LEU* 1.3 59.8 + - - +
98K ARG* 4.0 2.0 + - - +
128K ARG* 6.1 3.0 - - - +
130K GLU* 2.9 40.1 + - + +
132K VAL* 4.0 18.4 - - + -
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Residues in contact with LEU 97 (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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33K ILE* 3.1 34.3 - - + +
35K ALA 5.0 1.3 - - - +
95K ILE* 3.8 7.6 - - + -
96K LYS* 1.3 72.8 - - - +
98K ARG* 1.3 70.7 + - - +
108K PRO* 4.6 17.0 - - + -
112K ALA* 4.5 19.7 - - + -
129K ILE* 5.8 2.7 - - + -
130K GLU 3.1 17.6 + - - +
131K ASP* 3.3 13.8 - - + +
132K VAL 2.5 33.0 + - - -
133K THR* 3.9 0.6 + - - +
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Residues in contact with ARG 98 (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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32K HIS* 6.4 1.1 - - + -
33K ILE 2.9 9.7 + - - +
34K MET* 3.4 43.2 - - - +
35K ALA* 3.5 13.9 + - - +
96K LYS 5.2 2.0 - - - +
97K LEU* 1.3 85.6 - - - +
99K ALA* 1.3 69.5 + - - +
100K LYS* 3.0 35.3 - - - +
101K GLY 3.1 10.1 - - - +
102K GLY 4.7 0.8 - - - +
108K PRO* 4.6 1.7 - - - +
132K VAL* 3.6 19.5 - - + +
133K THR* 3.5 11.4 - - - -
134K PRO* 3.5 18.3 - - - +
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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