Contacts of the helix formed by residues 131 - 140 (chain K) in PDB entry 6IY6
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 ASN 131 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89K LEU 3.0 24.5 + - - +
90K SER 5.1 1.2 + - - -
91K SER 3.8 6.5 + - - -
92K CYS* 4.1 9.6 - - - +
95K PHE* 3.3 26.2 - - + -
127K THR 2.9 12.0 + - - +
128K LEU* 3.4 17.2 - - - +
129K LYS 3.2 10.9 - - - +
130K GLY* 1.3 78.8 - - - +
132K ALA* 1.3 61.0 + - - +
133K ALA* 2.7 34.0 + - - +
134K TRP* 2.9 11.7 + - + -
135K GLN* 3.5 14.4 + - - +
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Residues in contact with ALA 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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92K CYS* 6.1 4.9 - - + -
130K GLY 3.9 1.4 + - - -
131K ASN* 1.3 73.0 + - - +
133K ALA* 1.3 57.7 + - - +
134K TRP 3.1 1.6 - - - -
135K GLN* 2.9 29.1 + - - +
136K GLU* 3.1 12.4 + - - +
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Residues in contact with ALA 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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92K CYS* 4.2 15.8 - - + +
95K PHE* 4.1 25.4 - - + -
131K ASN* 2.7 12.7 + - - +
132K ALA* 1.3 74.1 - - - +
134K TRP* 1.3 54.6 + - - +
136K GLU* 3.5 16.9 + - - +
137K GLN* 3.0 32.5 + - + +
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Residues in contact with TRP 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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95K PHE* 3.8 16.7 - - + -
99K ILE* 3.7 32.3 - - + -
128K LEU* 3.0 42.4 - - + +
129K LYS 4.3 0.2 - - - -
131K ASN* 2.9 10.3 + - - +
133K ALA* 1.3 75.4 - - - +
135K GLN* 1.3 66.6 + - - +
137K GLN* 3.1 13.4 + - - +
138K LEU* 3.1 57.4 + - + +
143K ALA* 3.8 20.0 - - + -
144K PRO* 4.6 0.2 - - + -
147K VAL* 3.5 22.4 - - + -
148K LYS* 4.2 6.3 - - - -
151K PHE* 3.4 48.8 - + + -
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Residues in contact with GLN 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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129K LYS* 3.3 44.7 + - - +
131K ASN 3.5 17.0 - - - +
132K ALA* 2.9 9.2 + - - +
134K TRP* 1.3 82.6 - - + +
136K GLU* 1.3 59.4 + - - +
138K LEU* 3.6 22.5 + - - +
139K LYS* 3.2 35.4 + - - +
151K PHE* 5.2 1.4 - - - -
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Residues in contact with GLU 136 (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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132K ALA 3.1 11.3 + - - +
133K ALA* 3.5 17.7 - - - +
135K GLN* 1.3 75.2 - - - +
137K GLN* 1.3 60.6 + - + +
139K LYS* 3.4 7.3 + - - +
140K GLN* 2.9 61.6 + - + +
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Residues in contact with GLN 137 (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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95K PHE* 4.1 18.7 - - + -
96K THR* 4.5 17.6 - - - +
99K ILE* 4.0 24.4 - - - +
133K ALA 3.0 16.2 + - - +
134K TRP* 3.4 11.9 - - + +
136K GLU* 1.3 76.0 - - + +
138K LEU* 1.3 51.6 + - - +
140K GLN* 3.6 2.6 - - - -
141K LYS* 2.8 11.6 + - - -
142K LYS* 2.8 51.0 + - + +
143K ALA* 3.3 24.6 + - + +
144K PRO* 3.7 9.9 - - - +
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Residues in contact with LEU 138 (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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134K TRP* 3.1 53.4 + - + +
135K GLN* 3.6 26.0 - - - +
136K GLU 3.3 0.2 - - - -
137K GLN* 1.3 73.6 - - - +
139K LYS* 1.3 66.7 + - + +
141K LYS* 3.1 20.7 + - - +
143K ALA* 3.8 20.0 - - + -
148K LYS* 4.1 33.6 + - + +
151K PHE* 4.6 11.2 - - + -
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Residues in contact with LYS 139 (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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135K GLN* 3.2 22.5 + - - +
136K GLU* 3.4 6.5 + - - +
138K LEU* 1.3 79.3 - - + +
140K GLN* 1.3 64.0 + - + +
141K LYS* 3.4 7.8 + - - +
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Residues in contact with GLN 140 (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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136K GLU* 2.9 51.8 + - + +
137K GLN* 4.2 3.7 - - - +
139K LYS* 1.3 75.2 - - + +
141K LYS* 1.3 69.9 + - - +
142K LYS* 3.4 31.9 + - + +
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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