Contacts of the helix formed by residues 234 - 245 (chain A) in PDB entry 1C9T
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 TYR 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A HIS* 3.8 31.0 - + - -
101A ASN* 2.5 47.7 + - - -
103A ILE* 3.6 34.8 - - + -
179A ASN* 3.0 27.6 + - + +
229A THR* 3.6 18.4 - - + -
230A LYS 3.1 29.8 - - - -
231A VAL* 2.8 6.8 + - - +
233A ASN* 1.3 85.4 - - + +
235A VAL* 1.3 64.6 + - - +
236A SER 3.2 2.9 - - - -
237A TRP* 3.2 12.0 + + + +
238A ILE* 2.9 24.5 + - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.4 11.9 - - + -
124A PRO* 3.4 36.8 - - + +
125A THR* 5.9 0.9 - - - -
231A VAL* 3.3 10.0 + - + +
232A CYS* 3.4 23.8 + - - +
233A ASN 3.6 1.6 - - - -
234A TYR* 1.3 75.4 - - - +
236A SER* 1.3 65.3 + - - +
238A ILE* 3.2 10.5 + - - +
239A LYS* 2.8 51.4 + - + +
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASN 5.2 2.9 + - - -
234A TYR 3.2 0.6 - - - -
235A VAL* 1.3 77.1 - - - +
237A TRP* 1.3 65.0 + - - +
239A LYS* 2.8 11.9 + - - +
240A GLN* 2.8 24.2 + - - +
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Residues in contact with TRP 237 (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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89A ILE* 3.8 33.4 - - + -
91A HIS* 3.8 50.5 - + + +
92A PRO* 3.9 16.8 - - + +
103A ILE* 3.9 26.7 - - + -
105A LEU* 3.7 26.9 - - + -
234A TYR* 3.2 15.2 + - + +
236A SER* 1.3 78.4 - - - +
238A ILE* 1.3 81.4 + - + +
240A GLN* 3.2 6.7 + - + +
241A THR* 2.8 44.9 + - - -
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Residues in contact with ILE 238 (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 ILE* 3.8 20.9 - - + -
53A VAL* 4.8 3.4 - - + -
103A ILE* 4.3 13.7 - - + -
105A LEU* 3.9 17.7 - - + -
123A LEU* 3.8 31.2 - - + -
231A VAL* 4.1 13.5 - - + -
234A TYR 2.9 27.8 + - - +
235A VAL* 3.4 9.0 - - - +
237A TRP* 1.3 89.5 - - + +
239A LYS* 1.3 65.7 + - - +
241A THR* 3.2 1.2 + - - -
242A ILE* 3.1 45.0 + - + +
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Residues in contact with LYS 239 (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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123A LEU* 4.7 14.8 - - + -
125A THR* 6.2 2.6 - - - +
235A VAL* 2.8 34.8 + - + +
236A SER* 2.8 12.2 + - - +
238A ILE* 1.3 76.8 - - - +
240A GLN* 1.3 61.2 + - - +
242A ILE* 3.4 8.9 + - + +
243A ALA* 3.2 22.5 + - - +
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Residues in contact with GLN 240 (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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236A SER 2.8 15.6 + - - +
237A TRP* 3.9 9.4 - - + +
239A LYS* 1.3 72.3 - - - +
241A THR* 1.3 64.0 + - - +
243A ALA* 3.1 17.1 + - - +
244A SER* 2.9 45.1 + - - +
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Residues in contact with THR 241 (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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51A TRP* 4.2 2.6 - - + -
89A ILE* 3.7 30.1 - - + -
105A LEU* 3.6 24.0 - - + -
237A TRP* 2.8 43.9 + - + -
240A GLN* 1.3 76.6 - - - +
242A ILE* 1.3 61.7 + - - +
244A SER* 4.8 0.7 - - - -
245A ASN* 2.7 46.7 + - - +
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Residues in contact with ILE 242 (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 ILE* 4.5 17.7 - - + -
48A ASN* 4.5 10.1 - - - +
51A TRP* 3.8 48.0 + - + +
105A LEU* 4.5 2.9 - - + -
123A LEU* 5.6 1.6 - - + -
238A ILE* 3.1 39.9 + - + +
239A LYS* 3.8 7.6 - - + +
241A THR* 1.3 77.8 - - - +
243A ALA* 1.3 65.8 + - - +
244A SER 3.3 1.0 + - - -
245A ASN* 3.5 14.9 + - - +
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Residues in contact with ALA 243 (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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239A LYS 3.2 10.3 + - - +
240A GLN* 3.1 17.1 + - - +
242A ILE* 1.3 80.3 - - - +
244A SER* 1.3 60.0 + - - +
245A ASN* 4.8 1.9 - - - +
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Residues in contact with SER 244 (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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240A GLN* 2.9 38.6 + - - +
241A THR* 5.1 0.4 - - - -
243A ALA* 1.3 76.5 - - - +
245A ASN* 1.3 71.9 + - - +
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Residues in contact with ASN 245 (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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51A TRP* 3.6 17.9 - - + -
87A LYS* 3.8 19.5 + - - +
89A ILE* 3.6 14.7 - - + +
107A LYS* 2.9 40.5 + - + +
241A THR* 2.7 45.7 + - - +
242A ILE 3.5 12.1 + - - +
243A ALA 4.8 1.6 - - - +
244A SER* 1.3 89.8 - - - +
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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