Contacts of the strand formed by residues 122 - 128 (chain D) in PDB entry 2P5E
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 122 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ASP* 3.7 10.1 - - - +
121D PRO* 1.3 75.9 - - - +
123D VAL* 1.3 66.1 + - - +
124D TYR* 3.7 31.1 + - + +
138D LEU 3.3 1.9 - - - +
139D PHE* 3.3 6.8 - - - -
140D THR* 2.9 33.2 + - - +
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Residues in contact with VAL 123 (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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122D ALA* 1.3 74.2 - - - +
124D TYR* 1.3 64.0 + - - +
137D CYS* 4.0 3.6 - - + -
138D LEU 3.0 4.5 - - - +
139D PHE* 3.5 25.1 - - + -
187D CYS* 3.4 41.1 - - + +
188D ALA* 5.8 1.3 - - - +
191D PHE* 3.5 37.0 - - + -
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Residues in contact with TYR 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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120D ASP* 4.4 5.0 + - - -
122D ALA* 3.7 25.9 - - + +
123D VAL* 1.3 79.6 - - - +
125D GLN* 1.3 61.7 + - - +
126D LEU* 3.8 9.2 - - + +
137D CYS* 3.3 5.0 - - - +
138D LEU* 2.7 40.3 + - + +
140D THR* 3.6 32.3 - - + -
141D ASP* 5.3 0.4 - - - -
187D CYS* 4.8 1.6 - - - -
128E SER* 3.8 14.1 - - - -
130E ALA* 3.6 19.1 - - + -
131E GLU* 3.4 46.9 - - + -
134E HIS* 3.8 25.2 - + - +
135E THR* 4.0 8.9 - - + +
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Residues in contact with GLN 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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124D TYR* 1.3 74.2 - - - +
126D LEU* 1.3 63.5 + - - +
127D ARG* 3.8 22.4 + - - +
135D SER* 3.3 29.1 + - - +
136D VAL 3.6 2.7 - - - -
187D CYS* 3.9 27.7 - - + +
128E SER* 3.6 20.5 + - - -
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Residues in contact with LEU 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 TYR* 3.8 23.1 - - + +
125D GLN* 1.3 81.6 - - - +
127D ARG* 1.3 61.0 + - - +
135D SER* 3.1 7.9 - - - -
136D VAL* 3.0 35.6 + - + +
138D LEU* 3.8 20.6 - - + -
125E PHE* 3.5 19.8 - - + +
126E GLU 3.2 19.3 - - - +
128E SER* 4.2 8.7 - - - +
131E GLU* 5.5 1.1 - - - +
139E THR 3.3 25.4 - - - +
141E VAL* 3.5 28.7 - - + -
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Residues in contact with ARG 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 GLN* 3.8 22.0 + - - +
126D LEU* 1.3 75.9 - - - +
128D ASP* 1.3 67.8 + - - +
129D SER 3.3 0.2 + - - -
132D SER* 3.1 41.9 + - - -
134D LYS 3.6 1.1 - - - -
135D SER* 3.1 22.5 + - - -
125E PHE* 3.7 2.2 - - - -
126E GLU* 2.8 38.5 + - + +
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Residues in contact with ASP 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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127D ARG* 1.3 74.1 - - - +
129D SER* 1.3 75.0 + - - +
130D LYS* 3.0 16.1 + - - +
131D SER* 3.1 48.9 + - - +
132D SER* 3.8 4.0 + - - -
134D LYS* 2.9 40.4 + - + +
123E ALA* 3.8 18.0 - - - +
124E VAL 3.4 7.7 + - - +
125E PHE* 3.3 16.6 - - + -
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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