Contacts of the strand formed by residues 105 - 111 (chain C) in PDB entry 2XWT
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 HIS 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A TRP* 4.1 1.2 - - - -
98A ASN 3.4 21.1 + - - -
99A TYR* 3.5 12.5 - + + -
100A ASN* 4.3 1.6 - - - -
79C SER 3.2 3.3 + - - +
80C ARG* 3.3 11.1 - - + +
81C ILE 3.0 26.5 + - - +
82C TYR* 2.9 32.3 - + - +
103C VAL* 3.8 1.3 - - - +
104C THR* 1.3 87.0 - - - +
106C ILE* 1.3 67.9 + - - +
107C GLU* 3.2 38.9 + - + -
128C LEU* 3.8 0.6 - - - +
130C PHE* 3.3 39.3 + + + +
132C GLY 5.5 0.2 - - - -
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Residues in contact with ILE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ILE* 3.3 9.2 - - + +
92C LEU* 6.4 0.2 - - + -
97C PHE* 3.5 50.5 - - + -
103C VAL* 3.6 22.9 - - + -
105C HIS* 1.3 76.6 - - - +
107C GLU* 1.3 72.2 + - - +
108C ILE* 4.6 7.6 - - + -
122C LEU* 4.1 15.3 - - + -
125C LEU* 4.1 13.0 - - + -
128C LEU* 3.9 13.0 - - + -
130C PHE 3.2 6.4 + - - +
131C LEU* 3.3 22.2 - - + +
132C GLY 3.0 21.8 + - - -
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 5.7 0.2 + - - -
97A TRP* 3.1 22.7 + - + +
98A ASN* 4.6 4.7 + - - +
99A TYR* 4.4 3.8 - - - -
81C ILE 3.1 7.6 + - - +
82C TYR* 3.4 12.7 - - + -
83C VAL 2.9 25.7 + - - +
105C HIS* 3.2 33.3 + - + -
106C ILE* 1.3 74.9 - - - +
108C ILE* 1.3 69.8 + - - +
109C ARG* 2.9 34.2 + - + +
132C GLY* 3.2 13.1 - - - +
134C PHE* 3.5 14.0 - - - -
157C GLU* 4.2 10.6 - - - +
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ILE* 5.4 1.6 - - + -
81C ILE* 5.9 0.7 - - + +
83C VAL* 3.4 31.2 - - + -
89C LEU* 4.7 4.0 - - + -
92C LEU* 4.4 23.3 - - + -
97C PHE* 4.3 20.6 - - + -
106C ILE* 4.6 9.0 - - + -
107C GLU* 1.3 76.0 - - - +
109C ARG* 1.3 62.1 + - - +
111C THR* 3.6 31.4 - - + +
114C LEU* 4.1 15.3 - - + -
117C ILE* 6.3 0.4 - - + -
131C LEU* 6.1 0.7 - - + -
132C GLY 2.9 9.1 + - - +
133C ILE* 3.4 14.8 - - + +
134C PHE* 2.9 25.2 + - - +
136C THR* 4.7 1.3 - - + +
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TRP* 3.6 19.2 - - - -
52A TYR* 3.9 4.4 - - - -
54A ASP* 2.9 28.8 + - - -
56A ASP* 3.0 36.4 + - - +
58A ARG* 4.0 2.0 - - - +
97A TRP* 3.9 14.2 - - + -
83C VAL 2.8 16.9 + - - +
84C SER* 3.3 23.3 - - - +
85C ILE 3.0 19.4 + - - -
107C GLU* 2.9 29.5 + - + +
108C ILE* 1.3 77.3 - - - +
110C ASN* 1.3 74.3 + - - +
111C THR* 3.5 5.5 - - - +
134C PHE* 3.2 43.9 - - + +
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Residues in contact with ASN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 2.8 41.0 + - - +
84C SER* 3.6 15.6 + - - -
85C ILE* 3.3 19.9 - - + +
86C ASP 3.1 24.3 + - - +
87C VAL* 5.3 1.7 - - - +
109C ARG* 1.3 76.0 - - - +
111C THR* 1.3 59.2 + - - +
112C ARG* 3.8 3.9 + - - -
134C PHE* 2.9 11.3 + - - +
135C ASN* 2.9 41.9 - - - +
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Residues in contact with THR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C VAL* 4.3 5.4 - - + -
86C ASP* 3.4 25.6 - - + +
89C LEU* 4.1 17.7 - - + -
108C ILE* 3.6 19.5 - - + +
109C ARG 3.7 9.9 - - - +
110C ASN* 1.3 81.7 + - - +
112C ARG* 1.3 59.2 + - - +
113C ASN 3.2 3.4 - - - -
114C LEU* 3.0 40.9 + - - +
135C ASN 3.0 5.0 + - - -
136C THR* 3.3 21.8 - - - +
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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