Contacts of the helix formed by residues 126 - 135 (chain A) in PDB entry 1R1P
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A TYR* 3.4 13.2 - - - -
124A PHE* 3.7 7.1 - - - +
125A PRO* 1.3 82.7 - - - +
127A LEU* 1.3 64.7 + - - +
128A ASN 3.4 1.9 + - - -
129A LYS* 3.1 18.0 + - - +
130A LEU* 3.1 18.7 + - - +
508A SO4 2.7 39.5 + - - -
91B PRO* 6.4 2.0 - - - -
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Residues in contact with LEU 127 (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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60A TRP* 4.0 27.6 - - + -
84A ILE* 4.3 25.1 - - + -
94A PHE* 5.5 3.1 - - + -
96A ILE* 4.8 0.9 - - + -
109A VAL* 4.4 21.3 - - + -
117A TYR* 3.7 23.4 - - + -
126A SER* 1.3 73.2 - - - +
128A ASN* 1.3 58.0 + - - +
130A LEU* 3.1 18.6 + - + +
131A VAL* 2.9 32.6 + - + +
91B PRO* 3.5 32.8 + - + +
92B GLY* 4.1 6.5 - - - +
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Residues in contact with ASN 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 SER* 3.2 1.8 + - - -
127A LEU* 1.3 79.2 - - - +
129A LYS* 1.3 56.3 + - - +
131A VAL* 3.4 8.7 + - - +
132A ASP* 2.9 48.7 + - - +
135A ARG* 5.8 1.0 + - - -
508A SO4 2.7 36.1 + - - +
91B PRO* 5.9 0.6 - - - +
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Residues in contact with LYS 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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124A PHE* 4.0 19.1 - - + -
125A PRO* 3.7 29.7 - - + +
126A SER* 3.1 15.0 + - - +
128A ASN* 1.3 76.6 - - - +
130A LEU* 1.4 58.3 + - - +
132A ASP* 3.4 8.5 + - - +
133A TYR* 3.0 29.1 + - - +
508A SO4 3.2 29.5 + - - +
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Residues in contact with LEU 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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96A ILE* 4.1 26.2 - - + -
109A VAL* 4.6 7.6 - - + -
117A TYR* 3.6 11.0 - - + +
118A PHE* 3.6 41.5 - - - +
119A LEU* 4.0 10.8 - - + -
124A PHE* 3.6 21.4 - - + -
126A SER 3.1 13.6 + - - +
127A LEU* 3.1 11.9 + - + +
129A LYS* 1.4 73.0 - - - +
131A VAL* 1.3 72.8 + - + +
133A TYR* 3.3 2.6 + - - +
134A TYR* 3.2 45.4 + - + -
147A LEU* 5.7 1.3 - - + -
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Residues in contact with VAL 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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82A PHE* 3.9 24.0 - - + -
84A ILE* 3.9 27.1 - - + -
96A ILE* 5.0 1.8 - - + -
127A LEU* 2.9 22.2 + - + +
128A ASN* 3.7 10.5 - - - +
129A LYS 3.3 0.2 - - - -
130A LEU* 1.3 83.6 - - + +
132A ASP* 1.3 66.8 + - - +
134A TYR* 3.0 13.5 + - - -
135A ARG* 3.2 32.1 + - - +
147A LEU* 3.9 16.4 - - + +
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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 ASN* 2.9 39.8 + - - +
129A LYS* 3.8 8.4 - - + +
130A LEU 3.3 0.2 - - - -
131A VAL* 1.3 75.8 - - - +
133A TYR* 1.3 61.9 + - - +
135A ARG* 2.9 49.2 + - - +
136A THR* 4.0 5.7 + - - +
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Residues in contact with TYR 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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122A GLU* 4.0 23.7 - - + +
124A PHE* 3.2 39.0 - + + -
129A LYS 3.0 12.9 + - - +
130A LEU 3.6 2.9 - - - +
131A VAL 3.3 0.2 - - - -
132A ASP* 1.3 76.0 - - - +
134A TYR* 1.4 91.0 + + - +
136A THR* 3.2 10.0 + - - -
137A THR* 3.0 49.0 + - - +
500A SO4 2.5 30.3 + - - -
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Residues in contact with TYR 134 (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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119A LEU* 3.8 29.0 + - + -
120A TRP* 3.5 21.6 + + - +
122A GLU 4.9 3.5 + - - -
124A PHE* 4.5 4.5 - + - -
130A LEU* 3.2 30.6 + - + +
131A VAL 3.0 5.0 + - - -
133A TYR* 1.4 95.2 - + - +
135A ARG* 1.3 60.6 + - - +
136A THR 3.3 1.3 - - - -
137A THR* 3.3 23.1 - - + +
138A SER 3.6 10.8 - - - -
139A ILE* 3.6 23.1 - - + -
145A VAL 4.4 0.7 - - - +
146A PHE* 3.5 4.0 - - - -
147A LEU* 2.9 44.0 + - + -
500A SO4 2.7 39.7 + - - -
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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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82A PHE* 4.7 2.3 - - - -
128A ASN* 5.8 1.0 + - - -
131A VAL* 3.2 27.4 + - - +
132A ASP* 2.9 40.5 + - - +
134A TYR* 1.3 80.0 - - - +
136A THR* 1.4 65.3 + - + +
146A PHE* 3.4 20.1 - - - +
147A LEU* 3.6 26.0 + - + +
148A ARG* 4.4 2.0 - - - +
149A ASP* 2.8 50.1 + - - +
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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