Contacts of the strand formed by residues 111 - 115 (chain D) in PDB entry 2XTJ
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 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A SER* 3.7 21.5 - - - +
374A ASP* 3.7 20.9 - - - +
378A CYS* 4.3 5.4 - - + -
379A PHE 3.3 12.3 - - - +
380A VAL* 3.9 17.5 - - + -
102D ILE 3.5 0.9 - - - +
103D GLN* 3.1 7.3 + - - +
104D ILE* 3.0 50.1 + - + +
105D GLY* 3.8 16.6 - - - -
106D ARG* 5.2 0.4 - - - +
109D MET* 4.4 12.6 - - + -
110D ASN* 1.3 78.5 - - - +
112D TYR* 1.3 59.6 + - - +
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Residues in contact with TYR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 6.3 0.4 - - + -
377A THR 4.2 0.5 - - - +
378A CYS* 3.5 2.3 - - - -
379A PHE* 2.7 41.3 + - - +
380A VAL* 6.3 0.2 - - - -
381A SER* 6.2 1.1 - - - -
54D ILE* 3.7 38.9 - - + +
55D LEU* 3.7 35.4 - - + -
101D GLU* 4.5 19.1 - - + -
102D ILE 3.7 1.1 - - - -
103D GLN* 3.6 37.5 + - + -
110D ASN* 3.1 29.5 + - - -
111D VAL* 1.3 75.7 - - - +
113D TYR* 1.3 58.8 + - - +
114D LEU* 3.8 3.1 + - + +
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A CYS* 3.3 25.1 - - + -
377A THR* 3.6 8.1 - - - -
378A CYS* 3.7 14.8 - - - -
32B ALA* 5.6 0.3 - - - +
50B ASN* 5.4 0.5 + - - -
91B PHE* 3.3 35.2 + - - -
92B ASP 5.7 0.7 - - - -
100D TYR 3.3 3.3 - - - +
101D GLU* 3.4 1.4 - - - -
102D ILE* 2.9 47.9 + - + +
104D ILE* 3.8 25.4 - - + -
111D VAL 3.7 1.2 + - - -
112D TYR* 1.3 70.5 - - - +
114D LEU* 1.3 78.7 + - - +
115D MET* 3.4 31.2 + - + +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A THR* 2.8 41.3 + - - +
379A PHE* 3.8 19.7 - - + -
91B PHE 5.2 0.9 - - - +
52D ASN* 3.2 36.3 - - + +
55D LEU* 4.2 11.0 - - + -
59D ASN* 3.4 31.0 - - - +
99D HIS* 4.6 1.1 - - + -
100D TYR 3.3 4.0 - - - +
101D GLU* 4.0 22.4 - - + -
112D TYR* 4.7 4.3 - - + +
113D TYR* 1.3 74.3 - - - +
115D MET* 1.3 61.6 + - - +
116D TYR* 3.8 28.3 + - + +
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Residues in contact with MET 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASN* 5.5 2.0 - - - -
91B PHE* 4.2 12.6 - - + -
99D HIS* 3.4 2.2 - - - +
100D TYR* 3.0 62.2 + - + +
102D ILE* 4.6 14.6 - - + -
113D TYR* 3.4 42.8 + - + +
114D LEU* 1.3 71.3 - - - +
116D TYR* 1.3 59.5 + - - +
117D ARG* 3.0 58.0 + - + +
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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