Contacts of the strand formed by residues 123 - 129 (chain D) in PDB entry 2ESV
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 ALA 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D ASP 3.7 7.4 - - - +
122D PRO* 1.3 74.8 - - - +
124D VAL* 1.3 64.7 + - - +
125D TYR* 3.4 37.5 - - + +
139D LEU 3.4 1.4 - - - +
140D PHE* 3.5 5.4 - - - -
141D THR* 3.1 32.3 + - - +
201D THR* 4.0 2.9 - - - +
202D PHE* 3.4 24.2 - - + +
140E HIS* 4.9 0.4 - - + -
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Residues in contact with VAL 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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123D ALA* 1.3 71.2 - - - +
125D TYR* 1.3 64.2 + - - +
126D GLN 4.3 0.2 + - - -
138D CYS* 4.5 1.3 - - + -
139D LEU 3.3 5.8 - - - +
140D PHE* 3.6 26.7 - - + -
188D CYS* 3.4 37.1 - - + +
192D PHE* 4.0 26.2 - - + -
197D ILE* 5.4 1.6 - - + -
201D THR* 4.1 4.5 - - + -
202D PHE 3.0 9.3 + - - -
203D PHE* 3.6 31.9 - - + -
204D PRO* 3.1 23.4 - - - +
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Residues in contact with TYR 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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123D ALA* 3.4 21.4 - - + +
124D VAL* 1.3 74.6 - - - +
126D GLN* 1.3 61.5 + - - +
127D LEU* 3.9 9.9 - - + +
138D CYS* 3.5 4.7 - - - +
139D LEU* 2.9 35.9 + - + +
141D THR* 3.7 25.8 - - + -
142D ASP* 5.5 0.2 - - - -
188D CYS* 3.8 4.9 - - - -
202D PHE* 3.9 14.4 - + - -
204D PRO* 3.8 7.4 - - + -
134E SER* 3.5 28.5 - - - -
136E ALA* 3.6 16.2 - - + -
137E GLU* 3.4 39.3 - - + -
140E HIS* 3.2 33.8 - - - +
141E THR* 3.6 8.6 - - + +
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Residues in contact with GLN 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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124D VAL 4.3 0.4 + - - -
125D TYR* 1.3 74.3 - - - +
127D LEU* 1.3 67.3 + - - +
128D ARG* 3.0 40.9 + - + +
136D SER* 4.6 16.4 + - - +
137D VAL 3.7 8.5 - - - +
138D CYS* 5.6 0.2 - - - -
186D PHE 5.4 4.9 + - - -
187D ALA* 5.8 1.4 - - - +
188D CYS* 3.8 26.4 - - + +
204D PRO* 5.7 1.0 - - - +
134E SER* 3.5 21.5 + - - -
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Residues in contact with LEU 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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125D TYR* 3.9 13.9 - - + +
126D GLN* 1.3 82.5 - - - +
128D ARG* 1.3 62.9 + - - +
136D SER* 3.7 4.3 + - - -
137D VAL* 2.9 36.0 + - + +
139D LEU* 3.6 32.1 - - + -
131E PHE* 3.7 21.1 - - + +
132E GLU 3.3 19.3 - - - +
134E SER* 4.1 8.7 - - - +
137E GLU* 5.5 0.4 - - - +
145E THR 3.2 27.1 - - - +
147E VAL* 3.6 24.7 - - + -
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Residues in contact with ARG 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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126D GLN* 3.0 40.8 + - + +
127D LEU* 1.3 79.4 - - - +
129D ASP* 1.3 63.7 + - - +
135D LYS* 3.6 36.2 - - + +
136D SER* 5.2 3.4 + - - +
131E PHE* 3.9 2.9 - - - -
132E GLU* 2.7 38.9 + - + +
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Residues in contact with ASP 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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128D ARG* 1.3 78.2 - - - +
130D SER* 1.3 76.3 + - - +
131D LYS* 3.1 25.6 + - - +
132D SER 3.9 11.6 - - - +
134D ASP* 4.6 6.4 - - - +
135D LYS* 3.3 51.2 + - + +
129E ALA* 4.2 16.2 - - - +
130E VAL 3.0 22.9 + - - +
131E PHE* 3.6 9.0 - - + -
132E GLU* 5.0 2.8 - - - +
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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