Contacts of the helix formed by residues 60 - 65 (chain L) in PDB entry 1S9C
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 PHE 60 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L TYR* 3.7 20.0 - + - -
22L TYR* 3.6 45.1 - + + -
26L GLU* 3.8 25.6 - - + -
27L ALA* 4.2 2.7 - - - -
30L TYR* 3.7 36.4 - + + -
56L CYS* 3.4 23.8 - - - -
57L LEU 2.9 17.7 + - - +
58L PRO 2.8 1.0 + - - -
59L THR* 1.3 77.8 + - - +
61L GLY* 1.3 57.8 + - - +
62L VAL 3.0 0.2 - - - -
63L ILE* 2.9 37.5 + - + +
64L ILE* 3.3 22.4 + - + +
100L LEU* 4.2 2.0 - - + -
191L SER* 5.6 0.2 - - - -
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Residues in contact with GLY 61 (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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58L PRO 3.1 8.2 + - - -
59L THR 2.9 1.8 - - - -
60L PHE* 1.3 77.3 - - - +
62L VAL* 1.3 63.8 + - - +
64L ILE* 3.2 19.3 + - - +
65L GLY 3.2 2.3 + - - -
94L LEU* 4.0 11.0 - - - -
96L LEU* 4.9 0.2 - - - -
100L LEU* 3.3 17.7 - - - +
138L CYS* 4.6 4.5 - - - -
140L ASN* 3.0 24.0 + - - -
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Residues in contact with VAL 62 (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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30L TYR* 5.3 1.8 - - + +
59L THR 2.9 15.6 + - - +
61L GLY* 1.3 77.3 - - - +
63L ILE* 1.3 59.4 + - + +
65L GLY 4.0 1.0 - - - -
66L GLN* 2.9 29.2 + - - +
92L GLN* 4.2 15.7 - - - +
94L LEU* 3.8 15.2 - - + +
140L ASN* 3.6 10.3 - - - +
142L PHE* 4.1 4.8 - - + -
188L TYR* 5.6 1.8 - - - +
217L LEU* 3.3 42.2 - - + -
220L PHE* 3.6 30.3 - - + -
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Residues in contact with ILE 63 (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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20L TYR* 3.4 33.2 - - + +
30L TYR* 3.1 42.4 - - + -
60L PHE* 2.9 20.4 + - + +
62L VAL* 1.3 80.6 - - + +
64L ILE* 1.3 65.8 + - - +
66L GLN* 3.4 24.3 + - - +
67L LYS* 3.6 7.8 + - - +
188L TYR* 4.4 8.7 - - + +
191L SER* 3.2 39.3 - - - +
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Residues in contact with ILE 64 (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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18L PHE* 3.6 18.2 - - - -
20L TYR* 3.8 37.9 - - + +
22L TYR* 3.8 13.2 - - + -
60L PHE* 3.3 15.9 + - + +
61L GLY* 3.2 15.0 + - - +
63L ILE* 1.3 80.9 - - - +
65L GLY* 1.3 59.4 + - - +
66L GLN 3.3 0.2 - - - -
67L LYS* 3.6 5.0 - - - +
100L LEU* 3.9 24.9 - - + -
106L LEU* 3.6 32.3 - - + -
108L CYS* 4.1 3.4 - - - -
130L SER* 3.5 23.1 - - - +
138L CYS* 4.5 1.6 - - - -
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Residues in contact with GLY 65 (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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18L PHE* 3.9 13.2 - - - -
61L GLY 3.2 8.3 + - - -
64L ILE* 1.3 79.1 - - - +
66L GLN* 1.3 61.9 + - - +
67L LYS 3.3 1.3 - - - -
68L SER* 4.4 1.4 + - - -
69L MET* 5.2 1.7 - - - +
108L CYS* 4.9 0.2 - - - -
126L MET* 4.6 4.7 - - - +
128L VAL* 4.1 19.9 - - - +
130L SER* 4.7 1.6 - - - -
140L ASN* 3.7 15.5 - - - +
142L PHE* 3.4 20.5 - - - -
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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