Contacts of the helix formed by residues 126 - 135 (chain K) in PDB entry 3CXC
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6970 G 3.6 41.1 - - - -
6980 A 3.6 4.4 + - - -
107K LYS* 4.4 6.1 - - - -
108K VAL 3.5 9.1 + - - -
109K LEU* 3.9 1.1 - - - -
110K GLY 3.4 13.3 + - - -
125K PHE* 1.3 75.7 - - - +
127K GLU* 1.3 70.1 + - - +
129K ALA* 3.0 26.9 + - - +
130K ARG* 3.0 14.6 + - - +
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Residues in contact with GLU 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6970 G 3.2 17.3 + - - +
126K SER* 1.3 74.7 - - - +
128K GLY* 1.3 65.5 + - - +
130K ARG* 3.0 17.2 + - - +
131K GLU* 3.0 35.7 + - + +
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Residues in contact with GLY 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6970 G 5.2 0.6 + - - -
6980 A 3.6 19.8 + - - -
110K GLY* 4.1 7.0 - - - -
126K SER* 3.3 0.8 - - - -
127K GLU* 1.3 79.5 - - - +
129K ALA* 1.3 62.0 + - - +
131K GLU* 4.0 8.5 - - - +
132K LYS* 3.1 36.5 + - - +
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Residues in contact with ALA 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K VAL* 4.5 4.5 - - + -
108K VAL* 3.7 22.7 - - + +
109K LEU 4.0 2.7 - - - -
110K GLY* 3.8 15.7 - - - +
125K PHE* 4.2 7.4 - - + -
126K SER* 3.0 32.3 + - - +
128K GLY* 1.3 78.2 - - - +
130K ARG* 1.3 67.0 + - - +
132K LYS* 3.9 1.2 - - - +
133K VAL* 3.1 27.5 + - + +
140K VAL* 5.2 0.9 - - - -
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Residues in contact with ARG 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K PHE* 3.8 25.0 + - + +
126K SER 3.0 13.8 + - - +
127K GLU* 3.0 10.9 + - - +
129K ALA* 1.3 71.9 - - - +
131K GLU* 1.3 68.9 + - + +
133K VAL* 2.8 14.6 + - - -
134K GLU* 2.9 29.8 + - - +
140K VAL* 4.2 27.6 - - + +
142K LEU* 4.0 30.3 - - - +
149K ARG* 3.2 36.4 - - - +
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Residues in contact with GLU 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K GLU* 3.0 43.2 + - + +
128K GLY* 4.0 6.5 + - - +
130K ARG* 1.3 75.2 - - + +
132K LYS* 1.3 58.3 + - + +
134K GLU* 3.1 10.6 + - - +
135K GLY* 2.7 34.3 + - - -
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Residues in contact with LYS 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6990 C 3.1 24.5 + - - -
66K VAL* 4.7 4.5 - - + -
110K GLY 3.1 29.1 + - - +
112K GLY 2.6 31.2 + - - +
113K GLN* 5.1 0.7 - - - -
114K VAL* 3.5 24.6 - - + +
128K GLY* 3.1 21.5 + - - +
129K ALA* 3.9 2.5 - - - +
131K GLU* 1.3 81.9 - - + +
133K VAL* 1.3 63.5 + - - +
135K GLY* 3.4 2.8 + - - +
136K ALA* 3.4 20.8 + - - +
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Residues in contact with VAL 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K VAL* 4.4 12.1 - - + -
114K VAL* 4.6 14.1 - - + -
118K LEU* 3.2 31.7 + - + +
120K LEU* 3.5 27.1 - - + -
125K PHE* 6.0 0.2 - - + -
129K ALA 3.1 18.7 + - - +
130K ARG 2.8 12.6 + - - +
132K LYS* 1.3 72.1 - - - +
134K GLU* 1.3 57.1 + - - +
136K ALA* 3.4 8.8 + - - +
138K GLY* 2.8 24.9 + - - -
139K SER* 3.5 22.4 - - - +
140K VAL* 4.1 8.7 - - + -
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Residues in contact with GLU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K ARG* 2.9 32.7 + - + +
131K GLU* 3.7 10.9 + - - +
133K VAL* 1.3 72.5 - - + +
135K GLY* 1.3 55.6 + - - +
136K ALA 2.9 4.5 - - - -
137K GLY* 2.7 27.0 + - - -
138K GLY 3.2 20.8 + - - +
139K SER* 5.1 4.9 - - - -
140K VAL* 5.4 6.7 + - + +
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Residues in contact with GLY 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K GLU 2.7 20.5 + - - -
132K LYS* 3.8 4.5 - - - -
133K VAL 3.4 0.2 - - - -
134K GLU* 1.3 70.1 - - - +
136K ALA* 1.3 55.7 + - - +
137K GLY 3.3 2.0 - - - -
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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