Contacts of the strand formed by residues 193 - 198 (chain T) in PDB entry 3P71
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 THR 193 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84T PHE* 3.6 6.0 - - - -
93T GLN* 3.2 30.5 + - + +
95T VAL* 3.8 28.3 - - + -
191T LEU 3.0 15.2 + - - -
192T PRO* 1.3 74.3 + - - +
194T LEU* 1.3 64.5 + - - +
195T LEU* 4.0 5.1 + - + +
220T PHE* 3.3 32.5 - - + -
222T ARG 3.2 6.9 + - - -
223T ALA* 3.2 5.9 - - - +
224T MET 2.8 25.1 + - - +
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Residues in contact with LEU 194 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T ILE* 4.0 26.7 - - + -
84T PHE* 3.5 29.2 - - + -
93T GLN 2.9 8.0 + - - +
94T ILE* 3.2 19.6 - - + +
95T VAL 2.8 25.8 + - - -
193T THR* 1.3 73.9 - - - +
195T LEU* 1.3 67.2 + - - +
196T ILE* 3.8 24.9 - - + -
224T MET* 3.4 30.3 - - + -
226T ILE* 3.6 26.5 - - + -
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Residues in contact with LEU 195 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95T VAL* 3.3 22.9 - - + +
97T LEU* 3.9 20.4 - - + -
193T THR* 4.1 13.2 - - + +
194T LEU* 1.3 77.1 - - - +
196T ILE* 1.3 64.5 + - - +
197T ALA 4.3 0.2 - - - -
215T TRP* 4.3 15.3 - - + -
216T ALA* 4.0 25.8 - - + -
220T PHE* 4.1 26.5 - - + -
223T ALA* 4.7 0.2 - - + -
224T MET 2.8 18.6 + - - +
225T PHE* 3.4 19.3 - - + -
226T ILE 2.9 25.8 + - - +
273T TRP* 4.5 7.9 - - + -
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Residues in contact with ILE 196 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77T VAL* 4.5 12.3 - - + -
81T ILE* 3.7 29.4 - - + -
94T ILE* 3.8 16.2 - - + -
95T VAL 3.0 7.3 + - - -
96T ASN* 3.7 23.1 - - + +
97T LEU* 2.6 37.7 + - - +
118T TYR* 4.8 7.6 - - - +
194T LEU* 3.8 23.1 - - + -
195T LEU* 1.3 80.0 - - - +
197T ALA* 1.3 60.8 + - - +
198T GLU* 4.0 20.2 - - + +
226T ILE* 3.7 15.9 - - + +
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Residues in contact with ALA 197 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T LEU* 3.9 10.8 - - + +
196T ILE* 1.3 71.9 - - - +
198T GLU* 1.3 59.8 + - - +
199T CYS 3.4 4.1 + - - -
200T VAL* 4.5 11.3 + - + -
201T LEU* 3.9 23.6 - - + +
212T LEU* 6.2 0.2 - - + -
225T PHE* 3.7 28.0 - - + -
226T ILE* 2.8 10.5 + - - -
227T ASN* 3.5 5.5 - - - +
228T TYR 3.1 23.1 + - - -
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Residues in contact with GLU 198 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C AN6 2.9 43.7 + - - +
37T LYS* 3.0 16.4 + - - -
73T ARG* 2.6 36.0 + - - +
74T VAL* 5.0 3.8 - - - +
77T VAL* 4.0 33.3 - - + +
96T ASN* 5.3 3.3 + - - +
97T LEU 4.4 1.8 + - - -
102T ASP* 5.0 6.2 - - - +
196T ILE* 3.8 16.0 + - + +
197T ALA* 1.3 69.8 - - - +
199T CYS* 1.3 72.0 + - - +
200T VAL* 3.5 4.6 - - - +
226T ILE* 6.2 0.4 - - - -
228T TYR* 4.1 10.8 - - + -
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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