Contacts of the strand formed by residues 110 - 118 (chain C) in PDB entry 1A6Z
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 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C CYS* 3.8 18.8 - - + -
103C GLU 3.7 13.0 - - - +
104C MET* 4.1 9.3 - - + +
108C ASN 3.4 10.8 + - - -
109C SER* 1.3 74.3 - - - +
111C GLU* 1.3 84.1 + - - +
112C GLY 4.3 0.2 - - - -
161C LEU 4.3 3.4 - - - +
162C GLU* 4.5 17.7 + - + +
166C PRO* 3.6 37.5 - - + +
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Residues in contact with GLU 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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102C CYS* 3.3 1.0 - - - -
103C GLU* 2.7 54.1 + - + +
105C GLN* 6.3 1.8 - - + -
109C SER 5.5 0.4 - - - +
110C THR* 1.3 86.1 - - - +
112C GLY* 1.3 61.5 + - - +
113C TYR* 4.6 2.6 - - - -
129C ASP* 5.3 4.9 - - - +
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Residues in contact with GLY 112 (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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101C GLY 3.5 10.1 - - - -
102C CYS* 4.2 2.9 - - - -
110C THR* 4.3 0.4 - - - +
111C GLU* 1.3 80.3 + - - +
113C TYR* 1.3 67.6 + - - +
128C PRO* 4.0 16.9 - - - +
161C LEU* 3.9 23.9 + - - -
162C GLU* 5.7 4.6 - - - +
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Residues in contact with TYR 113 (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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7C SER* 5.5 2.8 + - - -
8C LEU 4.1 1.4 + - - -
9C HIS* 2.9 31.2 + - - +
99C ILE* 3.4 36.1 - - + +
100C LEU* 3.3 4.8 - - - -
101C GLY* 3.1 52.7 + - - +
102C CYS* 4.0 9.8 + - - -
103C GLU* 4.8 5.8 - - + -
111C GLU 4.6 2.7 - - - -
112C GLY* 1.3 81.1 - - - +
114C TRP* 1.3 64.2 + - - +
115C LYS* 5.2 13.9 - - + +
125C GLU* 5.6 3.6 - - + +
126C PHE 5.2 5.4 - - - +
161C LEU* 3.4 13.6 - - - +
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Residues in contact with TRP 114 (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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72C TRP* 4.2 14.6 - + - -
75C MET* 3.9 28.9 - - + -
98C VAL* 3.8 17.6 - - + +
99C ILE 3.4 4.0 - - - -
100C LEU* 3.8 22.1 - - + +
113C TYR* 1.3 76.7 - - - +
115C LYS* 1.3 63.4 + - - +
116C TYR* 3.1 37.2 + + - -
125C GLU* 3.7 1.8 - - - +
126C PHE* 2.8 51.8 + + + +
133C TRP* 5.8 0.4 - - - -
157C ASN* 3.4 49.8 - - + -
160C TYR* 4.3 17.5 - + + -
161C LEU* 4.0 20.0 - - + -
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Residues in contact with LYS 115 (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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98C VAL* 3.3 8.1 - - - +
99C ILE* 2.7 52.9 + - + +
113C TYR* 5.3 12.3 - - + +
114C TRP* 1.3 75.1 - - - +
116C TYR* 1.3 64.3 + - - +
122C ASP* 5.0 13.9 - - - +
124C LEU 3.7 2.9 - - - +
125C GLU* 3.2 48.1 + - + +
58D LYS* 6.3 0.8 - - - +
60D TRP* 3.8 15.8 - - + -
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Residues in contact with TYR 116 (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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79C ASP* 3.1 33.3 + - + -
83C ILE* 4.2 14.4 - - + -
96C LEU* 4.4 8.3 - - + -
97C GLN 3.6 1.8 - - - -
98C VAL* 4.0 25.4 - - + -
114C TRP* 3.1 41.1 + + - -
115C LYS* 1.3 78.4 - - - +
117C GLY* 1.3 59.4 + - - +
122C ASP* 3.8 0.7 - - - -
123C HIS* 2.9 27.6 + - + -
124C LEU* 2.7 32.2 + - + +
133C TRP* 4.5 8.7 - + - -
147C TRP* 3.5 36.3 - + - -
153C ARG* 3.2 12.3 + - - -
157C ASN* 5.2 0.3 + - - -
60D TRP* 3.7 6.1 - - - -
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Residues in contact with GLY 117 (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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95C THR 4.0 0.2 - - - +
96C LEU* 3.4 7.4 - - - +
97C GLN* 2.7 42.7 + - - +
116C TYR* 1.3 74.4 - - - +
118C TYR* 1.3 59.8 + - - -
119C ASP 4.1 0.6 + - - -
120C GLY 4.7 2.0 - - - -
121C GLN 3.2 12.3 - - - -
60D TRP* 3.5 23.8 - - - -
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Residues in contact with TYR 118 (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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80C PHE* 4.3 4.7 - + - -
83C ILE* 3.4 26.0 - - + -
84C MET* 3.3 21.2 - - + +
87C HIS* 3.5 34.5 - + - -
89C HIS* 2.7 32.1 + + - -
94C HIS* 3.3 24.4 - - + -
95C THR 3.3 16.8 - - - -
96C LEU* 4.5 8.1 - - + -
117C GLY* 1.3 71.5 - - - -
119C ASP* 1.3 86.7 + - + +
121C GLN* 2.9 23.5 + - - +
123C HIS* 3.8 25.7 - - + +
137C GLU* 5.7 1.1 - - - -
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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