Contacts of the helix formed by residues 131 - 140 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89L LEU 3.0 24.7 + - - +
90L SER 5.1 1.2 + - - -
91L SER 3.8 6.1 + - - -
92L CYS* 4.1 10.4 - - - +
95L PHE* 3.3 26.8 - - + -
127L THR 2.9 13.2 + - - +
128L LEU* 3.4 18.2 - - - +
129L LYS 3.2 10.5 - - - +
130L GLY* 1.3 76.7 - - - +
132L ALA* 1.3 62.7 + - - +
133L ALA* 2.7 33.5 + - - +
134L TRP* 2.9 12.3 + - + -
135L GLN* 4.0 11.3 + - - +
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Residues in contact with ALA 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L CYS* 5.9 5.1 - - + +
130L GLY 3.9 2.6 + - - +
131L ASN* 1.3 72.2 + - - +
133L ALA* 1.3 56.8 + - - +
134L TRP 3.1 1.6 - - - -
135L GLN* 2.9 28.7 + - - +
136L GLU* 3.1 11.9 + - - +
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Residues in contact with ALA 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L CYS* 4.2 15.6 - - + +
95L PHE* 4.1 25.1 - - + -
131L ASN* 2.7 12.6 + - - +
132L ALA* 1.3 75.5 - - - +
134L TRP* 1.3 54.9 + - - +
136L GLU* 3.2 18.2 + - - +
137L GLN* 3.0 29.9 + - + +
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Residues in contact with TRP 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L PHE* 3.8 16.2 - + + -
99L ILE* 3.7 32.1 - - + -
128L LEU* 3.0 42.4 - - + +
131L ASN* 2.9 10.2 + - - +
133L ALA* 1.3 75.2 - - - +
135L GLN* 1.3 70.8 + - - +
137L GLN* 3.1 13.1 + - - +
138L LEU* 3.1 55.5 + - + +
143L ALA* 3.8 20.4 - - + -
144L PRO* 4.6 0.4 - - + -
147L VAL* 3.5 22.0 - - + -
148L LYS* 4.2 7.2 - - - -
151L PHE* 3.4 44.9 - + + -
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Residues in contact with GLN 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L LYS* 3.7 43.5 - - - +
131L ASN 4.0 5.1 + - - +
132L ALA* 2.9 10.1 + - - +
134L TRP* 1.3 86.9 + - - +
136L GLU* 1.3 56.6 + - - +
138L LEU* 3.6 22.4 + - - +
139L LYS* 3.2 43.7 + - + +
151L PHE* 5.2 1.4 - - - -
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Residues in contact with GLU 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L ALA 3.1 11.3 + - - +
133L ALA* 3.2 19.8 - - - +
134L TRP 3.2 0.2 - - - -
135L GLN* 1.3 75.4 - - - +
137L GLN* 1.3 78.1 + - - +
139L LYS* 3.4 7.2 + - - +
140L GLN* 2.9 67.4 + - - +
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Residues in contact with GLN 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L PHE* 4.1 18.9 - - - -
96L THR* 4.5 17.2 - - - +
99L ILE* 4.0 24.4 - - - +
133L ALA* 3.0 16.0 + - + +
134L TRP* 3.1 11.6 + - - +
136L GLU* 1.3 83.7 + - - +
138L LEU* 1.3 53.8 + - - +
140L GLN* 3.6 3.0 - - - -
141L LYS 2.8 11.6 + - - -
142L LYS* 2.8 49.7 + - + +
143L ALA* 3.3 24.5 + - + +
144L PRO* 3.7 10.4 - - - +
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Residues in contact with LEU 138 (chain L).
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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359B GLY 5.3 0.5 - - - +
134L TRP* 3.1 56.3 + - + +
135L GLN* 3.6 26.9 - - - +
137L GLN* 1.3 73.4 - - - +
139L LYS* 1.3 65.9 + - + +
141L LYS* 3.1 24.8 + - - +
143L ALA* 3.8 20.0 - - + -
148L LYS* 4.1 31.0 + - + +
151L PHE* 4.7 10.5 - - + -
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Residues in contact with LYS 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B GLY 3.5 25.7 - - - +
360B VAL* 5.3 3.2 - - - +
361B GLU* 2.5 47.8 + - + +
135L GLN* 3.2 26.7 + - + +
136L GLU* 3.4 7.2 + - - +
138L LEU* 1.3 80.2 - - + +
140L GLN* 1.3 62.7 + - + +
141L LYS* 3.4 6.6 + - - +
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Residues in contact with GLN 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L GLU* 2.9 53.9 + - + +
137L GLN* 4.2 3.7 - - - +
139L LYS* 1.3 74.8 - - + +
141L LYS* 1.3 69.5 + - - +
142L LYS* 3.3 23.8 + - + +
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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