Contacts of the helix formed by residues 127 - 137 (chain A) in PDB entry 5P21
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 SER 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ARG* 3.1 15.0 + - - +
125A VAL 3.6 2.2 + - - -
126A GLU* 1.3 72.1 + - - +
128A ARG* 1.3 58.8 + - - +
130A ALA* 3.1 3.3 + - - +
131A GLN* 2.8 31.3 + - - +
141A TYR* 4.0 10.3 - - - -
143A GLU* 2.8 32.3 + - - -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.1 8.2 - - + +
127A SER* 1.3 79.9 - - - +
129A GLN* 1.3 61.5 + - - +
131A GLN* 3.4 11.0 + - + +
132A ASP* 3.0 39.7 + - - +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE* 3.7 23.7 - - + -
124A THR 4.1 4.9 - - - +
125A VAL* 3.7 18.5 - - + -
126A GLU* 3.1 48.4 + - + +
128A ARG* 1.3 80.2 - - - +
130A ALA* 1.4 61.3 + - - +
132A ASP* 3.5 11.0 + - - +
133A LEU* 3.0 22.7 + - - +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 3.8 15.5 - - + -
90A PHE* 3.9 16.6 - - + -
113A LEU* 3.7 4.1 - - + +
125A VAL* 4.6 2.0 - - + -
126A GLU 3.3 9.3 + - - +
127A SER 3.1 5.2 + - - +
129A GLN* 1.4 76.9 - - - +
131A GLN* 1.3 57.2 + - - +
133A LEU* 3.2 3.1 + - - +
134A ALA* 2.9 29.3 + - - +
141A TYR* 3.4 38.4 - - + +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A SER* 2.8 20.9 + - - +
128A ARG* 3.7 12.3 - - + +
130A ALA* 1.3 73.8 - - - +
132A ASP* 1.3 57.3 + - - +
134A ALA* 3.4 4.5 + - - +
135A ARG* 2.8 35.5 + - + +
139A ILE 5.3 1.2 + - - -
140A PRO* 6.0 0.2 - - - +
141A TYR* 3.5 39.8 - - + +
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.0 30.2 + - - +
129A GLN* 3.5 11.2 - - - +
131A GLN* 1.3 74.0 - - - +
133A LEU* 1.3 64.8 + - - +
135A ARG* 3.3 7.0 + - - +
136A SER* 3.0 22.9 + - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE* 3.7 33.2 - - + +
93A ILE* 4.3 15.3 - - + -
94A HIS* 5.8 1.3 - - + +
113A LEU* 4.3 6.3 - - + -
129A GLN 3.0 13.8 + - - +
130A ALA 3.2 8.5 + - - +
132A ASP* 1.3 75.5 - - - +
134A ALA* 1.3 63.0 + - - +
136A SER* 2.8 25.8 + - - +
137A TYR* 3.1 49.5 + - + +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.9 12.5 - - + +
130A ALA 2.9 16.7 + - - +
131A GLN* 3.7 6.3 - - - +
133A LEU* 1.3 75.3 - - - +
135A ARG* 1.3 63.2 + - - +
137A TYR* 3.0 4.5 + - - +
138A GLY 3.0 18.4 + - - -
139A ILE* 3.2 37.1 + - + +
140A PRO 4.3 0.2 - - - -
141A TYR* 3.7 23.6 - - + +
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLN* 2.8 23.6 + - + +
132A ASP* 3.6 8.7 - - - +
134A ALA* 1.3 76.5 - - - +
136A SER* 1.4 59.8 + - - +
138A GLY* 3.2 14.0 + - - -
139A ILE 5.0 1.3 - - - -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASP 3.0 13.5 + - - -
133A LEU* 2.8 24.6 + - - +
135A ARG* 1.4 75.5 - - - +
137A TYR* 1.3 70.1 + - - +
138A GLY 3.8 0.2 + - - -
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 4.0 19.0 - - + +
94A HIS* 3.4 44.1 + + - +
97A ARG* 3.5 58.0 + - + +
98A GLU* 5.9 0.4 - - - -
107A ASP 5.4 0.7 - - - +
111A MET* 5.8 0.2 - - - -
113A LEU* 5.4 1.8 - - + -
133A LEU* 3.1 43.2 + - + +
134A ALA* 3.0 9.4 + - - +
136A SER* 1.3 85.6 - - - +
138A GLY* 1.3 61.3 + - - +
139A ILE* 3.6 29.8 + - + +
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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