Contacts of the strand formed by residues 87 - 91 (chain X) in PDB entry 1T6B
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 VAL 87 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81X THR* 3.7 15.5 - - + +
83X ALA 3.2 20.6 - - - +
84X ASP 3.5 5.0 + - - +
85X ASN 3.4 3.6 + - - -
86X HIS* 1.3 80.6 - - - +
88X THR* 1.3 71.2 + - - +
89X MET* 4.3 1.8 - - + +
97X ILE* 3.6 19.3 - - + +
98X ASN* 3.6 3.6 - - - -
99X LYS* 3.2 23.7 + - - +
118X ILE* 3.8 17.3 - - + -
119X GLN 3.2 13.5 - - - +
120X TYR* 4.0 6.1 - - + -
132X PHE* 3.6 28.5 - - + -
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Residues in contact with THR 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X VAL* 1.3 77.1 + - - +
89X MET* 1.3 64.2 + - - +
90X TRP* 3.4 36.6 - - + -
95X GLU* 4.5 9.4 - - + +
97X ILE 3.5 11.0 - - - +
98X ASN* 4.0 18.3 + - - +
99X LYS* 4.1 8.3 + - - +
118X ILE* 3.5 1.9 - - - -
119X GLN* 2.8 62.3 + - - +
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Residues in contact with MET 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X PHE* 3.8 28.0 - - + -
81X THR* 5.2 2.0 - - - -
87X VAL* 4.6 2.7 - - + -
88X THR* 1.3 74.9 - - - +
90X TRP* 1.3 67.1 + - - +
91X VAL* 3.8 22.9 - - + -
95X GLU* 3.3 5.9 - - - +
96X VAL* 2.7 33.7 + - + -
97X ILE* 2.9 43.8 + - + +
116X ILE* 3.9 18.8 - - + -
117X LYS 3.3 11.0 - - - +
118X ILE* 3.7 22.4 - - + -
134X LEU* 4.1 16.4 - - + -
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Residues in contact with TRP 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X THR* 3.4 39.3 - - + -
89X MET* 1.3 78.5 - - - +
91X VAL* 1.3 67.3 + - - +
92X ASP 4.3 0.2 - - - -
93X ASP* 3.8 36.1 - - - +
94X GLN 3.1 5.2 - - - +
95X GLU* 3.4 32.8 + - + +
115X GLN 4.4 0.7 - - - -
116X ILE* 3.6 3.1 - - - -
117X LYS* 3.0 58.2 + - + +
119X GLN* 3.8 23.3 - - + -
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Residues in contact with VAL 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X ILE* 4.9 1.8 - - + -
79X PHE* 4.1 17.9 - - + -
89X MET* 3.8 15.7 - - + -
90X TRP* 1.3 77.7 - - - +
92X ASP* 1.3 72.8 + - + +
94X GLN* 2.9 24.9 + - - +
96X VAL* 4.3 14.8 - - + -
106X ILE* 4.2 19.7 - - + +
108X LEU* 4.4 11.7 - - + -
114X TYR* 4.4 18.2 - - + -
115X GLN 3.3 6.7 - - - +
116X ILE* 3.7 19.3 - - + -
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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