Contacts of the helix formed by residues 130 - 146 (chain A) in PDB entry 2C4P
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 ASP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ILE* 2.5 31.9 + - + +
128A LYS 3.3 0.6 - - - -
129A SER* 1.3 80.9 + - - +
131A LYS* 1.3 59.5 + - - +
132A GLU* 2.8 27.4 + - - +
133A LYS* 2.9 45.0 + - + +
134A TYR 3.4 9.9 + - - -
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Residues in contact with LYS 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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112A ASP* 5.6 0.2 + - - -
127A TYR* 2.7 75.4 + - + +
128A LYS* 4.9 7.4 + - - +
130A ASP* 1.3 69.1 + - - +
132A GLU* 1.3 67.1 + - - +
133A LYS 3.0 2.7 - - - -
134A TYR* 2.9 7.6 + - + -
135A ASN* 2.8 38.8 + - - +
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Residues in contact with GLU 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 ASP* 2.8 14.7 + - - +
131A LYS* 1.3 79.8 - - - +
133A LYS* 1.3 59.2 + - + +
135A ASN* 4.1 6.8 + - - +
136A ARG* 3.7 40.1 + - - +
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Residues in contact with LYS 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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126A ILE* 3.9 17.9 - - + -
130A ASP* 2.9 34.1 + - + +
132A GLU* 1.3 77.4 - - + +
134A TYR* 1.3 67.4 + - - +
135A ASN 3.3 0.2 - - - -
136A ARG* 3.1 24.6 + - - +
137A HIS* 3.1 23.2 + - - +
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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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45A TYR* 2.7 28.3 + + - -
74A TYR* 3.3 23.6 - + - -
75A HIS* 3.3 7.4 + - - -
76A PRO* 2.9 22.5 - - + +
110A LEU 4.7 0.8 + - - -
111A CYS 5.9 0.2 - - - -
113A PRO* 4.0 5.5 - - + +
123A ILE* 3.5 33.2 - - + -
126A ILE* 3.8 16.3 - - + +
127A TYR* 3.3 39.7 - + + -
130A ASP 3.4 5.2 + - - +
131A LYS* 2.9 15.5 + - - +
133A LYS* 1.3 79.5 - - - +
135A ASN* 1.3 82.2 + - - +
136A ARG 2.9 6.1 + - - -
137A HIS* 3.4 2.9 + - - -
138A ALA* 3.4 21.1 + - + +
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Residues in contact with ASN 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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44A ALA* 4.0 22.7 - - + +
127A TYR* 5.2 1.2 - - - -
131A LYS* 2.8 27.2 + - - +
132A GLU* 4.4 5.9 - - - +
133A LYS 3.3 0.4 - - - -
134A TYR* 1.3 98.4 - - - +
136A ARG* 1.3 59.7 + - - +
138A ALA 4.5 0.4 - - - -
139A ARG* 3.0 29.0 + - - +
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Residues in contact with ARG 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 GLU* 3.7 39.3 + - - +
133A LYS* 3.5 13.7 - - - +
134A TYR 3.0 0.8 - - - -
135A ASN* 1.3 79.7 - - + +
137A HIS* 1.3 70.5 + - + +
138A ALA 3.1 1.1 - - - -
139A ARG* 2.7 43.9 + - - +
140A GLU* 2.8 26.6 + - + +
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Residues in contact with HIS 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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74A TYR* 3.3 34.6 + + + -
126A ILE* 3.3 30.0 - - + +
133A LYS* 3.1 27.4 + - - +
136A ARG* 1.3 79.0 - - - +
138A ALA* 1.3 53.4 + - - +
140A GLU* 2.9 20.5 + - - +
141A TRP* 2.8 48.2 + - - +
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Residues in contact with ALA 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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44A ALA* 3.7 21.3 - - + -
45A TYR* 3.6 29.8 - - + +
74A TYR* 3.5 21.0 - - + +
134A TYR* 3.4 13.9 + - + +
135A ASN 4.7 0.2 - - - -
136A ARG 3.1 0.2 - - - -
137A HIS* 1.3 80.0 - - - +
139A ARG* 1.3 51.9 + - - +
141A TRP* 3.4 1.7 + - - +
142A THR* 2.5 38.6 + - - -
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Residues in contact with ARG 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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44A ALA* 3.3 25.8 - - - +
135A ASN 3.0 24.2 + - - +
136A ARG* 2.7 46.9 + - - +
138A ALA* 1.3 69.5 - - - +
140A GLU* 1.3 65.2 + - + +
142A THR* 3.1 13.6 + - - -
143A GLN* 3.1 19.2 + - - +
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Residues in contact with GLU 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 ARG* 2.8 21.9 + - + +
137A HIS* 3.2 34.7 + - - +
139A ARG* 1.3 76.8 - - + +
141A TRP* 1.3 63.4 + - + +
143A GLN* 3.7 11.6 - - - +
144A LYS* 3.1 31.4 + - - +
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Residues in contact with TRP 141 (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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72A LYS* 4.7 8.0 - - + +
73A ILE* 4.1 16.4 - - - -
74A TYR* 3.7 52.5 - + + +
137A HIS* 2.8 39.8 + - - +
138A ALA 3.7 3.8 - - - +
140A GLU* 1.3 82.1 - - + +
142A THR* 1.3 57.6 - - - +
144A LYS* 4.3 7.0 - - - +
145A TYR* 2.7 71.8 + + + +
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Residues in contact with THR 142 (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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44A ALA 3.6 0.4 + - - -
45A TYR* 3.3 32.1 - - - +
46A GLN 3.6 24.5 - - - +
48A GLY* 3.7 12.1 - - - -
50A PHE* 4.4 5.0 - - + -
138A ALA 2.5 25.4 + - - -
139A ARG* 3.1 9.6 + - - -
141A TRP* 1.3 77.0 - - - +
143A GLN* 1.3 58.4 + - + +
146A ALA* 2.8 36.4 + - + +
147A MET* 3.5 12.9 - - + +
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Residues in contact with GLN 143 (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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139A ARG 3.1 16.0 + - - +
140A GLU* 3.7 11.6 + - - +
142A THR* 1.3 75.9 - - - +
144A LYS* 1.3 61.0 + - + +
147A MET* 3.1 38.8 - - + +
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Residues in contact with LYS 144 (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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140A GLU* 3.1 26.8 + - - +
141A TRP* 3.3 9.3 + - - +
143A GLN* 1.3 80.0 - - + +
145A TYR* 1.3 107.8 + - + +
146A ALA 3.9 0.2 - - - -
147A MET 5.3 0.4 - - - -
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Residues in contact with TYR 145 (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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71A THR* 3.1 15.9 - - - +
72A LYS* 3.4 51.1 - - + +
141A TRP* 2.7 56.3 + + + +
144A LYS* 1.3 116.6 - - + +
146A ALA* 1.3 57.4 + - - +
147A MET 3.8 2.0 - - - +
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Residues in contact with ALA 146 (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 GLY 4.4 0.2 - - - +
48A GLY* 3.5 9.2 - - - -
49A VAL* 2.7 58.8 + - - +
50A PHE* 3.8 23.3 - - + -
71A THR* 3.9 0.7 - - + -
141A TRP 4.9 0.2 - - - +
142A THR* 2.8 18.6 + - - +
145A TYR* 1.3 80.1 - - - +
147A MET* 1.3 63.5 + - - +
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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