Contacts of the helix formed by residues 127 - 141 (chain A) in PDB entry 1RDC
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 HIS 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.2 16.8 - + + -
119A GLU* 4.3 18.2 + - - -
126A GLY* 1.3 82.4 - - - +
128A PRO* 1.3 76.3 - - + +
129A GLU* 3.3 12.2 + - - +
130A ASN* 3.5 19.7 - - - +
131A GLU* 3.1 24.7 + - - +
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Residues in contact with PRO 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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127A HIS* 1.3 97.4 - - + +
129A GLU* 1.3 77.6 + - - +
131A GLU* 3.5 17.0 - - + +
132A ARG* 3.5 21.0 + - - +
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Residues in contact with GLU 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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8A PHE* 4.0 26.5 - - + -
25A ILE* 3.8 8.1 - - + +
27A ARG* 2.9 41.6 + - - +
32A GLU* 4.5 1.9 - - - +
127A HIS* 3.3 5.6 - - - +
128A PRO* 1.3 99.9 - - - +
130A ASN* 1.3 59.9 + - - +
131A GLU 2.9 5.9 + - - -
132A ARG* 3.2 31.6 + - - +
133A CYS* 3.3 18.5 + - - -
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Residues in contact with ASN 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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8A PHE* 3.4 14.4 - - - +
9A THR 4.3 7.3 + - - +
10A ASP* 4.1 9.9 - - - +
68A SER* 2.5 45.9 + - - -
69A THR* 4.0 6.5 - - - +
70A ASN* 5.0 7.5 + - - +
121A VAL* 3.9 17.8 - - + +
124A HIS* 5.6 6.6 - - + -
126A GLY 3.6 17.7 - - - +
127A HIS* 3.5 19.4 + - - +
129A GLU* 1.3 77.0 - - - +
131A GLU* 1.4 58.1 + - - +
133A CYS* 3.4 20.9 - - - +
134A ASP* 3.7 4.9 + - - +
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Residues in contact with GLU 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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124A HIS* 4.9 17.3 + - + +
126A GLY 4.7 3.7 - - - +
127A HIS 3.1 20.9 - - - +
128A PRO* 3.5 17.9 - - + +
130A ASN* 1.4 78.3 - - - +
132A ARG* 1.3 60.4 + - - +
133A CYS 2.9 5.2 - - - -
134A ASP* 2.9 20.9 + - + +
135A GLU* 3.0 18.8 + - + +
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Residues in contact with ARG 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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25A ILE* 3.6 20.8 - - + +
32A GLU* 3.3 24.4 + - - -
34A THR* 2.8 33.5 + - - +
128A PRO 3.5 15.2 + - - +
129A GLU* 3.2 22.0 + - - +
131A GLU* 1.3 75.6 - - - +
133A CYS* 1.3 50.6 + - - +
135A GLU* 3.5 12.2 + - - +
136A LEU* 2.7 47.5 + - + +
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Residues in contact with CYS 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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8A PHE* 3.9 22.7 - - - -
9A THR 4.0 3.6 - - - +
10A ASP* 3.4 18.3 - - + +
23A GLY* 3.4 22.5 - - - +
25A ILE* 3.5 17.9 - - - -
129A GLU 3.3 15.3 - - - -
130A ASN* 3.4 12.6 - - - +
132A ARG* 1.3 74.4 - - - +
134A ASP* 1.3 58.0 - - - +
135A GLU 3.1 1.1 - - - -
136A LEU* 3.4 7.9 - - - +
137A ALA* 2.6 37.8 + - - +
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Residues in contact with ASP 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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10A ASP* 4.1 16.6 - - - +
12A SER* 5.1 3.1 - - - -
124A HIS* 5.2 13.3 - - + -
130A ASN 3.7 4.3 + - - +
131A GLU* 2.9 20.9 + - + +
133A CYS* 1.3 77.5 - - - +
135A GLU* 1.3 58.8 + - + +
137A ALA* 3.8 2.3 - - - +
138A ARG* 2.8 65.3 + - - +
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Residues in contact with GLU 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 GLU* 3.0 15.1 + - - +
132A ARG* 3.6 13.7 - - - +
134A ASP* 1.3 76.7 - - + +
136A LEU* 1.3 68.4 + - - +
138A ARG* 3.7 27.1 + - - +
139A ALA* 3.2 24.6 + - - +
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Residues in contact with LEU 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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22A TYR 4.7 0.2 - - - -
23A GLY* 3.9 13.5 - - - -
24A ALA 4.3 0.4 - - - +
25A ILE* 3.6 22.4 - - + -
34A THR* 3.2 33.9 - - + -
35A PHE 4.2 0.9 - - - +
36A SER* 3.6 26.1 + - - +
132A ARG* 2.7 32.3 + - + +
133A CYS* 3.4 6.1 - - - +
135A GLU* 1.3 75.0 - - - +
137A ALA* 1.3 61.4 + - - +
139A ALA* 3.8 3.7 - - - +
140A ALA* 3.3 21.5 + - - +
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Residues in contact with ALA 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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10A ASP* 4.1 2.9 - - + +
11A GLY* 4.1 4.5 - - - -
12A SER* 3.9 14.9 - - - +
21A GLY* 3.6 27.9 + - - +
22A TYR* 3.6 21.1 - - - +
23A GLY 3.7 2.2 - - - +
133A CYS 2.6 23.5 + - - +
134A ASP* 3.9 3.6 - - - +
136A LEU* 1.3 74.0 - - - +
138A ARG* 1.3 61.5 + - - +
140A ALA* 3.6 1.4 + - - -
141A ALA* 3.3 20.3 + - - +
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Residues in contact with ARG 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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12A SER* 3.7 21.3 - - - +
14A LEU* 5.1 4.1 - - + +
134A ASP* 2.8 58.3 + - - +
135A GLU* 3.4 30.4 + - - +
137A ALA* 1.3 74.5 - - - +
139A ALA* 1.3 57.8 + - - +
141A ALA* 3.8 11.5 - - - +
142A MET* 4.0 12.0 + - - +
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Residues in contact with ALA 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 GLU 3.2 17.4 + - - +
136A LEU* 3.8 4.5 - - - +
138A ARG* 1.3 72.5 - - - +
140A ALA* 1.3 62.1 + - - +
141A ALA 3.0 1.3 - - - -
142A MET* 2.6 36.5 + - - +
143A ASN* 3.4 8.3 + - - +
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Residues in contact with ALA 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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21A GLY* 4.1 2.9 - - - -
22A TYR 4.5 0.4 - - - +
36A SER* 3.7 12.1 - - - +
37A ALA* 3.6 30.7 - - - +
38A GLY* 3.3 10.0 - - - +
136A LEU 3.3 14.8 + - - +
137A ALA* 3.6 6.9 + - - +
139A ALA* 1.3 79.0 - - - +
141A ALA* 1.3 57.8 + - - +
143A ASN* 2.9 33.3 - - - +
144A PRO 3.3 1.4 - - - -
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Residues in contact with ALA 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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12A SER* 4.4 2.2 - - - +
14A LEU* 3.6 28.5 - - + +
19A PRO* 3.8 10.2 - - - +
20A GLY* 3.4 35.8 + - - +
21A GLY 3.9 0.2 - - - +
137A ALA 3.3 12.3 + - - +
138A ARG* 3.8 8.1 - - - +
139A ALA 3.0 0.2 - - - -
140A ALA* 1.3 80.6 - - - +
142A MET* 1.3 58.8 + - - +
143A ASN 3.2 4.2 + - - -
144A PRO* 3.5 15.2 - - - +
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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