Contacts of the strand formed by residues 123 - 130 (chain C) in PDB entry 2C11
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 GLU 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C LEU* 4.1 1.2 - - - +
101C LEU* 2.9 26.6 - - - +
102C GLN* 3.5 30.8 + - + +
121C ALA* 2.9 20.7 + - - +
122C ARG* 1.3 77.5 - - - +
124C ALA* 1.3 64.0 + - - +
142C VAL* 3.3 19.9 - - + +
143C VAL 3.6 11.4 - - - +
144C GLY* 4.6 0.2 - - - -
146C LEU* 3.6 7.9 - - - +
151C TYR* 2.8 34.7 + - - +
153C ARG* 4.8 6.6 + - - -
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.4 19.7 - - + -
71C VAL* 4.2 17.9 - - + -
99C VAL* 4.4 7.2 - - + -
100C GLU 2.8 16.4 - - - +
102C GLN* 3.5 5.8 - - - +
123C GLU* 1.3 76.6 - - - +
125C LEU* 1.3 61.1 + - - +
126C ALA 3.6 1.1 + - - -
141C LEU 3.6 0.3 - - - +
142C VAL* 3.6 1.8 - - - -
143C VAL* 2.9 32.2 + - + +
146C LEU* 4.0 8.5 - - + +
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Residues in contact with LEU 125 (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 SER 3.8 2.3 - - - +
99C VAL* 4.5 0.2 - - - -
100C GLU* 2.7 33.0 + - + +
101C LEU 5.2 0.7 - - - +
102C GLN* 3.7 19.9 - - + +
124C ALA* 1.3 71.5 - - - +
126C ALA* 1.3 60.0 + - - +
127C ILE* 4.0 8.9 + - + +
140C GLU* 3.3 32.3 - - + +
141C LEU 3.3 34.8 - - - +
142C VAL* 3.9 13.5 - - + +
155C VAL* 4.2 0.2 - - + -
159C ARG* 2.9 28.5 - - - +
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 4.0 19.5 - - + -
96C VAL* 4.7 2.7 - - + -
98C SER 3.1 9.4 - - - +
99C VAL* 3.8 21.3 - - + +
124C ALA 3.6 1.4 + - - -
125C LEU* 1.3 73.8 - - - +
127C ILE* 1.3 61.4 + - - +
128C VAL* 5.0 2.5 - - + -
139C SER 3.8 0.7 - - - +
140C GLU* 3.5 1.0 - - - -
141C LEU* 2.7 49.5 + - + +
143C VAL* 4.4 11.9 - - + -
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Residues in contact with ILE 127 (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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96C VAL* 3.5 2.8 - - - +
97C PHE* 2.8 34.8 + - + +
98C SER* 2.6 33.8 + - - +
125C LEU* 4.6 11.0 - - + +
126C ALA* 1.3 76.5 - - - +
128C VAL* 1.3 57.9 + - - +
129C PHE* 4.2 11.2 - - + -
138C VAL* 3.9 12.1 - - + -
139C SER 3.4 9.9 - - - +
140C GLU* 4.1 15.7 - - + +
344C PHE* 4.2 20.6 - - + -
647C VAL* 4.6 2.7 - - + -
648C PHE* 3.8 37.2 - - + -
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Residues in contact with VAL 128 (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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75C LEU* 5.4 0.4 - - + -
79C LEU* 4.2 7.0 - - + -
83C LEU* 5.0 4.5 - - + -
94C ASN 5.0 0.2 - - - -
95C CYS 3.1 17.3 - - - +
96C VAL* 3.6 27.8 - - + -
126C ALA* 5.0 3.1 - - + +
127C ILE* 1.3 78.5 - - - +
129C PHE* 1.3 76.6 + - - +
130C PHE* 3.6 34.6 + - + -
138C VAL* 3.3 3.8 - - - +
139C SER 2.9 35.5 + - - +
141C LEU* 4.2 20.0 - - + -
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Residues in contact with PHE 129 (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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93C ASP 3.4 1.4 - - - +
94C ASN* 3.2 6.1 - - - -
95C CYS* 2.9 38.5 + - - +
97C PHE* 3.2 41.7 - + + -
127C ILE* 4.2 3.6 - - + -
128C VAL* 1.3 80.2 - - - +
130C PHE* 1.3 59.9 + - - +
131C GLY 3.7 0.2 - - - -
137C ASN 4.3 0.4 - - - -
138C VAL* 4.0 17.9 - - + +
166C TYR* 3.4 20.0 - - + +
169C ARG* 3.5 34.1 - - + -
170C PRO* 3.5 28.9 - - + -
172C LEU* 3.3 36.8 - - + -
648C PHE* 5.1 0.7 - + - -
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Residues in contact with PHE 130 (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 LEU* 4.1 20.6 - - + -
83C LEU* 6.0 0.4 - - + -
94C ASN* 3.8 24.5 - - + +
128C VAL* 3.6 28.7 + - + -
129C PHE* 1.3 71.4 - - - +
131C GLY* 1.3 58.0 + - - +
132C ARG 3.8 0.7 - - - -
133C GLN* 3.1 24.2 - - - +
136C PRO* 3.2 19.3 - - - +
137C ASN* 3.0 33.4 + - - +
139C SER* 4.0 18.8 - - - -
141C LEU* 4.8 8.1 - - + -
154C ASP* 5.6 0.2 - - - -
166C TYR* 3.5 4.1 - - - -
1I NAG 3.3 35.9 - - - +
2I NAG 3.7 15.5 - - + -
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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