Contacts of the strand formed by residues 95 - 101 (chain A) in PDB entry 2XCH
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 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE* 4.1 20.2 - - + -
89A GLY 3.5 12.3 - - - +
90A GLU* 4.1 13.0 - - + +
91A GLY 5.3 0.5 + - - -
94A SER* 1.3 77.7 + - - +
96A VAL* 1.3 63.6 + - - +
97A VAL* 3.9 19.7 - - + -
110A ILE 3.6 1.7 - - - +
111A LYS* 4.4 0.2 - - - -
112A ILE* 2.7 47.3 + - - +
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Residues in contact with VAL 96 (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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87A ILE* 3.5 3.6 - - - +
88A LEU* 2.7 37.9 + - + -
89A GLY 2.8 21.4 + - - +
94A SER* 5.0 2.2 - - - +
95A THR* 1.3 75.3 - - - +
97A VAL* 1.3 58.8 + - - +
109A ALA* 3.8 29.4 - - + -
110A ILE 3.4 8.5 - - - +
111A LYS* 4.1 22.2 - - + +
1360A CKG 3.6 49.1 - - + +
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Residues in contact with VAL 97 (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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84A PHE* 3.9 24.9 - - + -
85A GLY 3.3 25.6 - - - +
86A LYS 3.4 6.5 - - - +
87A ILE* 4.0 10.5 - - + -
88A LEU* 4.3 4.5 - - - -
95A THR* 3.9 18.8 - - + -
96A VAL* 1.3 79.0 - - - +
98A LEU* 1.3 70.8 + - - +
99A ALA 3.6 0.3 + - - -
109A ALA* 3.7 0.3 - - - -
110A ILE* 2.8 34.5 + - - +
112A ILE* 4.0 18.4 - - + -
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Residues in contact with LEU 98 (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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85A GLY* 2.6 35.3 + - - -
86A LYS* 2.8 40.3 + - + +
88A LEU* 3.9 13.1 - - + +
97A VAL* 1.3 73.2 - - - +
99A ALA* 1.3 56.0 + - - +
107A GLU* 3.8 27.6 - - + +
108A TYR 3.6 13.9 - - - +
161A TYR* 3.5 55.2 - - + +
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Residues in contact with ALA 99 (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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82A PHE* 4.0 12.3 - - + -
83A LYS 3.4 7.4 - - - +
84A PHE* 4.0 16.6 - - + -
97A VAL 3.6 0.2 + - - -
98A LEU* 1.3 76.4 - - - +
100A ARG* 1.3 59.8 + - - +
101A GLU 4.1 0.6 + - - -
106A ARG 3.8 0.2 - - - +
107A GLU* 3.2 5.8 - - - +
108A TYR* 2.9 33.8 + - - +
110A ILE* 3.8 34.8 - - + -
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Residues in contact with ARG 100 (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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82A PHE* 3.2 2.7 - - - -
83A LYS* 2.8 54.1 + - + +
99A ALA* 1.3 73.0 - - - +
101A GLU* 1.3 64.6 + - - +
102A LEU* 3.4 1.9 + - + +
105A SER* 2.9 53.9 + - - +
106A ARG 3.4 3.8 - - - +
107A GLU* 3.2 37.5 + - + +
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Residues in contact with GLU 101 (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 LYS* 2.8 36.2 + - - +
81A ASP* 3.6 15.1 - - + +
82A PHE* 3.6 22.4 - - + -
99A ALA 4.1 0.2 - - - -
100A ARG* 1.3 71.6 - - - +
102A LEU* 1.3 59.8 + - - +
103A ALA* 4.3 10.5 - - + +
104A THR* 2.6 40.3 + - - +
105A SER* 2.8 34.5 + - - -
106A ARG* 2.9 14.1 + - - +
108A TYR* 3.8 20.1 + - + -
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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