Contacts of the helix formed by residues 130 - 141 (chain A) in PDB entry 1R6Q
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.7 11.6 - - - -
125A ARG* 5.4 2.5 - - - +
128A GLU 4.1 0.2 - - - -
129A VAL* 1.3 75.4 - - - +
131A ARG* 1.3 65.1 + - - +
132A LEU* 3.5 8.7 + - - +
133A ASP* 3.1 46.4 + - - +
134A VAL 3.4 4.0 + - - -
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Residues in contact with ARG 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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94A HIS* 4.6 15.2 + - - -
110A VAL* 3.8 38.1 - - + +
113A PHE* 3.7 36.6 - - + -
114A SER* 3.5 21.3 + - - -
130A SER* 1.3 72.4 - - - +
132A LEU* 1.3 63.2 + - - +
134A VAL* 3.2 6.8 + - - +
135A VAL* 3.0 25.4 + - + +
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Residues in contact with LEU 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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130A SER* 3.2 8.4 + - - +
131A ARG* 1.3 78.4 - - - +
133A ASP* 1.3 58.7 + - - +
135A VAL* 4.3 16.4 - - + -
136A ASN* 2.8 54.0 + - - +
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Residues in contact with ASP 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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47A CYS* 3.9 24.8 - - - -
128A GLU 3.7 13.7 - - - +
129A VAL* 3.9 1.0 - - + -
130A SER* 3.1 38.3 + - - +
132A LEU* 1.3 75.9 - - - +
134A VAL* 1.3 61.9 + - - +
136A ASN* 3.6 8.5 + - - +
137A PHE* 3.2 21.7 + - - +
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Residues in contact with VAL 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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43A ALA* 4.2 13.7 - - + -
44A LEU* 5.6 0.4 - - + -
47A CYS* 4.9 5.4 - - - -
106A ALA 3.9 12.3 - - - +
109A LEU* 4.1 24.2 - - + -
110A VAL* 3.6 21.8 - - + -
113A PHE* 4.1 13.9 - - + -
129A VAL* 3.8 20.0 - - + -
130A SER 3.8 12.1 - - - +
131A ARG 3.2 7.0 + - - +
133A ASP* 1.3 74.8 - - + +
135A VAL* 1.3 59.4 + - - +
137A PHE* 3.1 7.2 + - - +
138A ILE* 2.9 33.3 + - + +
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Residues in contact with VAL 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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110A VAL* 3.8 28.5 - - + -
131A ARG* 3.0 25.9 + - + +
132A LEU* 3.3 17.5 + - + +
134A VAL* 1.3 75.0 - - - +
136A ASN* 1.3 57.9 + - - +
138A ILE* 3.2 9.1 + - + +
139A SER* 2.9 42.5 + - - +
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Residues in contact with ASN 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 LEU* 2.8 48.2 + - - +
133A ASP* 3.8 9.1 + - - +
135A VAL* 1.3 74.1 - - - +
137A PHE* 1.3 56.4 + - - +
139A SER* 4.6 0.6 - - - -
140A HIS* 2.8 54.6 + - + +
141A GLY 3.7 2.0 + - - +
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Residues in contact with PHE 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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39A SER 4.8 3.1 - - - -
42A GLU* 3.8 24.0 - - + -
43A ALA* 3.6 37.0 - - + +
46A ALA* 3.5 27.8 - - + -
47A CYS* 5.7 1.6 - - - -
106A ALA* 5.7 1.8 - - + -
133A ASP 3.2 13.3 + - - +
134A VAL* 3.1 11.3 + - - +
136A ASN* 1.3 74.1 - - - +
138A ILE* 1.3 72.0 + - + +
141A GLY* 2.9 54.2 + - - -
142A THR 4.6 4.3 - - - -
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Residues in contact with ILE 138 (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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104A THR* 5.5 0.2 - - - +
106A ALA* 3.8 31.6 - - + +
107A ASN* 3.9 23.8 - - - +
110A VAL* 3.9 22.2 - - + -
134A VAL* 2.9 20.7 + - + +
135A VAL* 3.5 9.9 - - + +
137A PHE* 1.3 84.4 - - + +
139A SER* 1.3 62.4 + - - +
141A GLY 4.9 0.3 + - - -
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Residues in contact with SER 139 (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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135A VAL* 2.9 26.6 + - - +
136A ASN* 4.6 0.4 - - - -
138A ILE* 1.3 81.2 - - - +
140A HIS* 1.3 87.2 + - - +
141A GLY 3.9 0.2 - - - -
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Residues in contact with HIS 140 (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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136A ASN* 2.8 41.0 + - - +
139A SER* 1.3 96.4 + - - +
141A GLY* 1.3 62.4 + - - +
142A THR* 3.6 8.9 + - - +
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Residues in contact with GLY 141 (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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136A ASN 3.7 2.0 + - - +
137A PHE* 2.9 45.1 + - - +
138A ILE 4.9 0.2 + - - -
139A SER 3.9 0.2 - - - -
140A HIS* 1.3 74.0 - - - +
142A THR* 1.3 74.4 + - - -
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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