Contacts of the strand formed by residues 123 - 130 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D LEU* 4.1 4.3 - - - +
101D LEU* 3.8 8.7 - - - +
102D GLN* 3.2 38.7 + - + +
103D LEU 5.3 2.1 - - - +
104D PRO* 5.9 0.7 - - - +
105D PRO* 5.6 5.5 - - - +
121D ALA* 3.2 15.7 + - - +
122D ARG* 1.3 77.5 - - - +
124D ALA* 1.3 62.3 + - - +
142D VAL* 3.6 21.9 - - + +
143D VAL 3.2 11.0 - - - +
146D LEU* 4.6 2.7 - - - -
151D TYR* 3.0 36.4 + - + +
153D ARG* 3.5 23.1 + - - -
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 3.4 21.3 - - + -
71D VAL* 4.0 23.1 - - + -
99D VAL* 4.1 8.1 - - + -
100D GLU 3.1 15.9 - - - +
102D GLN* 3.8 4.7 - - - -
123D GLU* 1.3 75.1 - - - +
125D LEU* 1.3 59.4 + - - +
126D ALA* 3.9 0.4 + - - -
141D LEU 3.5 1.4 - - - +
142D VAL* 3.3 5.1 - - - -
143D VAL* 2.9 33.7 + - - +
146D LEU* 4.6 1.1 - - + -
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D SER* 3.7 2.6 + - - +
99D VAL* 3.3 2.8 + - - -
100D GLU* 3.0 36.0 + - + +
101D LEU 5.1 2.2 - - - +
102D GLN* 3.5 21.8 - - + +
124D ALA* 1.3 72.7 - - - +
126D ALA* 1.3 62.2 + - - +
127D ILE* 4.3 6.5 + - + +
140D GLU* 3.8 33.0 - - + +
141D LEU 3.5 18.6 - - - +
142D VAL* 4.1 11.9 - - + +
159D ARG* 3.0 33.4 - - - +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D VAL* 5.2 2.7 - - + -
75D LEU* 4.0 18.4 - - + -
96D VAL* 4.5 3.8 - - + -
98D SER 2.8 12.3 - - - +
99D VAL* 3.5 19.3 - - + -
124D ALA 3.9 0.8 + - - +
125D LEU* 1.3 74.5 - - - +
127D ILE* 1.3 61.4 + - - +
128D VAL* 3.8 6.9 + - + +
139D SER 3.4 3.5 - - - +
140D GLU* 3.6 2.0 - - - -
141D LEU* 3.0 36.8 + - + +
143D VAL* 5.2 3.8 - - + -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL* 3.7 2.3 - - - +
97D PHE* 2.9 34.7 + - + -
98D SER* 2.8 30.3 + - - +
125D LEU* 5.3 6.7 - - + +
126D ALA* 1.3 75.5 - - - +
128D VAL* 1.3 66.3 + - - +
129D PHE* 3.8 26.5 - - + -
138D VAL* 4.9 2.9 - - + -
139D SER 3.5 7.9 - - - +
140D GLU* 4.5 11.9 - - + +
344D PHE* 4.4 8.3 - - + -
647D VAL* 4.2 13.7 - - + -
648D PHE* 3.7 35.9 - - + -
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 5.4 1.1 - - + -
79D LEU* 3.8 20.2 - - + -
83D LEU* 4.3 1.8 - - + -
95D CYS 3.0 24.9 - - - +
96D VAL* 4.2 5.4 - - + -
126D ALA* 4.1 13.9 - - + +
127D ILE* 1.3 80.6 - - - +
129D PHE* 1.3 64.7 + - - +
130D PHE* 3.5 33.1 + - + -
138D VAL* 3.3 4.3 - - - +
139D SER* 3.0 31.6 + - - +
141D LEU* 3.9 27.1 - - + -
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Residues in contact with PHE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN* 3.4 4.7 - - - -
95D CYS* 2.8 51.7 + - - +
97D PHE* 3.3 35.7 - + + -
127D ILE* 3.8 12.8 - - + -
128D VAL* 1.3 76.4 - - - +
130D PHE* 1.3 63.9 + - - +
131D GLY 3.7 0.9 - - - -
137D ASN 3.9 3.6 - - - -
138D VAL* 3.4 19.3 - - + -
166D TYR* 3.6 16.4 - - + +
169D ARG* 3.3 37.2 - - + -
170D PRO* 3.7 18.8 - - + -
172D LEU* 3.6 28.3 - - + -
648D PHE* 5.4 0.4 - + - -
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU* 3.6 33.4 - - + -
83D LEU* 5.4 0.2 - - + -
94D ASN* 3.0 31.0 - - + +
128D VAL* 3.5 26.9 - - + -
129D PHE* 1.3 78.9 - - - +
131D GLY* 1.3 57.1 + - - +
132D ARG 3.4 0.4 - - - -
133D GLN* 3.2 24.2 - - - +
136D PRO* 3.0 25.1 - - - +
137D ASN* 2.7 20.8 + - - +
139D SER* 3.1 27.1 - - - -
141D LEU* 4.8 5.6 - - + -
166D TYR* 3.5 2.8 - - - -
1K NAG 3.3 39.7 - - - -
2K NAG 4.9 2.0 - - - -
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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