Contacts of the strand formed by residues 109 - 114 (chain A) in PDB entry 2XH1
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 MET 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 4.3 36.2 - - + +
91A GLN* 4.4 8.3 - - + -
92A ILE* 4.3 14.8 - - + -
97A PRO* 3.7 29.2 - - + -
99A THR* 3.1 33.7 + - + +
100A ILE* 3.7 25.4 - - + -
108A GLN* 1.3 84.0 + - - +
110A ASP* 1.3 63.1 + - - +
111A LEU* 5.3 1.6 - - + -
247A LEU* 5.1 2.5 - - + -
275A THR* 3.7 27.6 - - + -
276A GLY 3.8 6.1 - - - +
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.3 21.7 + - - +
108A GLN* 6.0 0.2 - - - -
109A MET* 1.3 77.0 - - - +
111A LEU* 1.3 77.3 + - - +
275A THR* 3.3 6.7 - - - +
276A GLY 2.9 32.8 + - - +
278A LYS* 3.5 52.9 + - + +
281A ILE* 3.9 16.8 - - + +
282A GLU* 5.3 0.7 + - - +
285A ILE* 4.7 7.4 - - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 4.8 4.2 - - - +
84A LEU* 3.8 26.0 - - + +
87A LEU* 3.8 44.2 - - + -
88A LYS* 3.9 23.5 + - + +
91A GLN* 3.7 30.7 - - + -
109A MET* 5.3 1.3 - - + -
110A ASP* 1.3 85.6 + - - +
112A CYS* 1.3 72.9 + - - +
273A PHE* 3.9 14.6 - - + -
274A LEU 3.1 13.0 - - - +
275A THR* 3.8 11.2 - - + +
281A ILE* 4.1 7.7 - - - +
285A ILE* 4.8 1.6 - - - +
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Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.6 16.4 - - - +
84A LEU* 4.0 2.5 - - - -
111A LEU* 1.3 78.8 - - - +
113A VAL* 1.3 64.1 + - - +
114A THR* 4.1 17.7 - - - -
273A PHE* 3.3 3.1 - - - +
274A LEU* 2.9 41.1 + - - +
281A ILE* 4.1 15.3 - - + -
284A VAL* 4.4 13.7 - - - -
285A ILE* 3.9 25.6 - - + -
288A ILE* 4.4 4.0 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER 4.4 1.0 - - - +
78A ALA 2.9 20.0 + - - +
79A GLY* 4.1 1.6 - - - -
83A LEU* 4.1 15.5 - - + -
84A LEU* 3.9 16.4 - - + -
87A LEU* 4.2 13.9 - - + -
112A CYS* 1.3 77.0 - - - +
114A THR* 1.3 65.6 + - - +
271A ILE* 3.8 23.1 - - + -
272A GLY 3.5 12.1 - - - +
273A PHE* 4.2 0.7 - - - -
288A ILE* 4.4 7.1 - - - +
295A PRO* 3.6 28.6 - - + +
300A GLN* 3.8 23.6 - - + +
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Residues in contact with THR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A CYS* 4.1 16.4 - - - +
113A VAL* 1.3 82.4 - - - +
115A SER* 1.3 60.8 + - - +
116A GLY 2.7 22.8 + - - -
117A SER* 4.1 2.6 - - - -
119A GLN* 3.7 9.2 - - - +
120A GLY* 3.9 25.6 + - - -
270A ARG 3.7 0.2 - - - +
271A ILE* 3.4 5.7 - - - -
272A GLY 2.9 37.0 + - - +
273A PHE* 3.8 3.1 + - - -
274A LEU* 4.3 7.4 - - + -
288A ILE* 4.0 18.8 - - + -
295A PRO* 4.3 5.9 - - - +
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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