Contacts of the helix formed by residues 231 - 244 (chain A) in PDB entry 3N7O
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 ILE 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.8 17.3 - - + -
53A LEU* 4.6 1.8 - - + -
103A ILE* 5.4 1.6 - - + -
123A PHE* 3.6 31.9 - - + -
209A ALA* 3.6 29.4 - - + +
210A GLN 3.0 14.1 + - - +
211A GLY* 3.6 36.8 - - - +
212A ILE* 3.8 17.7 - - + -
229A THR* 5.3 1.3 - - - -
230A ARG* 1.3 72.5 - - - +
232A SER* 1.3 66.7 + - - +
234A TYR* 2.8 19.9 + - - +
235A GLN* 3.3 15.3 + - + +
238A ILE* 4.4 6.7 - - + -
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Residues in contact with SER 232 (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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124A PRO* 5.8 2.8 - - - +
125A SER* 5.6 1.6 - - - -
210A GLN* 4.5 8.2 + - - +
230A ARG* 3.4 23.6 + - - +
231A ILE* 1.3 78.5 - - - +
233A HIS* 1.3 63.0 + - - +
234A TYR 3.2 0.9 + - - -
235A GLN* 3.2 34.1 + - - +
236A PRO* 4.0 4.5 - - - +
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Residues in contact with HIS 233 (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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178A ASN* 3.5 31.7 + - + +
179A LEU* 3.2 27.6 - - + +
230A ARG* 3.4 14.7 + - + +
231A ILE 3.0 0.2 + - - -
232A SER* 1.3 80.6 + - - +
234A TYR* 1.3 72.8 + + + +
235A GLN 3.9 0.2 + - - -
236A PRO* 3.9 9.1 - - - +
250A UNL 2.2 43.0 + - - -
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Residues in contact with TYR 234 (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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91A HIS* 3.6 32.8 - + - -
101A HIS* 2.8 49.8 + - - -
103A ILE* 3.8 26.2 - - + -
179A LEU* 3.8 19.7 + - - +
229A THR* 3.5 26.1 - - + +
230A ARG 3.2 23.3 - - - -
231A ILE 2.8 8.2 + - - +
233A HIS* 1.3 96.0 - + - +
235A GLN* 1.3 66.7 + - - +
236A PRO* 3.3 2.9 - - - -
237A TRP* 3.1 8.1 + - + +
238A ILE* 2.9 24.0 + - + +
250A UNL 3.7 7.9 - - - -
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Residues in contact with GLN 235 (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 PHE* 3.9 20.2 - - + +
124A PRO* 3.2 38.4 - - - +
125A SER* 3.5 15.7 + - - -
231A ILE* 3.7 17.7 - - + +
232A SER* 3.2 33.9 + - - +
234A TYR* 1.3 78.2 - - - +
236A PRO* 1.3 65.3 - - + +
238A ILE* 3.2 9.9 + - + +
239A ASN* 2.8 40.7 + - - +
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Residues in contact with PRO 236 (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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232A SER 4.0 5.2 - - - +
233A HIS 3.9 11.0 - - - +
234A TYR 3.5 3.6 - - - -
235A GLN* 1.3 93.4 - - + +
237A TRP* 1.3 56.6 + - - +
239A ASN* 3.3 10.4 + - + +
240A GLN* 2.9 27.9 + - - +
250A UNL 5.7 3.6 - - - +
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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 PHE 3.3 27.1 - - - -
90A ARG 4.0 3.1 - - - -
91A HIS* 3.6 42.0 - + + -
92A PRO* 3.5 20.9 - - + +
103A ILE* 4.1 27.8 - - + -
105A LEU* 4.0 27.6 - - + -
234A TYR* 3.1 10.0 + - + +
236A PRO* 1.3 75.1 - - - +
238A ILE* 1.3 86.2 + - + +
240A GLN* 3.1 27.0 + - - +
241A ILE* 3.0 47.5 + - + +
250A UNL 3.4 21.8 + - - +
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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* 4.2 12.3 - - + -
53A LEU* 3.9 17.3 - - + -
103A ILE* 4.3 9.4 - - + -
105A LEU* 4.0 17.9 - - + -
123A PHE* 3.8 33.2 - - + -
231A ILE* 4.4 5.6 - - + -
234A TYR 2.9 20.5 + - - +
235A GLN* 3.6 13.7 - - + +
237A TRP* 1.3 90.5 - - + +
239A ASN* 1.3 62.0 + - - +
241A ILE* 3.3 2.1 + - - +
242A LEU* 2.9 46.3 + - + +
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Residues in contact with ASN 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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48A ARG* 4.9 5.7 + - - -
235A GLN* 2.8 33.0 + - - +
236A PRO* 3.7 8.2 - - + +
238A ILE* 1.3 79.8 - - - +
240A GLN* 1.3 56.3 + - - +
242A LEU* 3.9 10.7 - - - +
243A GLN* 2.9 34.7 + - - +
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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 PRO 2.9 13.7 + - - +
237A TRP* 3.3 31.6 - - - +
239A ASN* 1.3 76.2 - - - +
241A ILE* 1.3 67.9 + - + +
243A GLN* 3.4 4.4 + - - +
244A ALA* 3.2 24.5 + - + +
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Residues in contact with ILE 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 PHE* 4.3 6.1 - - + -
89A PHE* 4.0 34.1 - - + -
105A LEU* 3.6 25.1 - - + -
237A TRP* 3.0 54.8 + - + +
238A ILE 3.7 0.7 - - - +
240A GLN* 1.3 82.9 - - + +
242A LEU* 1.3 62.5 + - - +
244A ALA* 3.3 9.1 + - + -
245A ASN* 2.9 37.3 + - - +
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Residues in contact with LEU 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* 4.4 7.4 - - + -
48A ARG* 3.7 43.3 - - + +
51A PHE* 3.6 47.0 - - + -
105A LEU* 4.7 4.0 - - + -
123A PHE* 5.7 0.7 - - + -
238A ILE* 2.9 39.5 + - + +
239A ASN* 3.9 9.4 - - - +
241A ILE* 1.3 75.7 - - - +
243A GLN* 1.3 62.3 + - - +
245A ASN* 3.1 23.6 + - - +
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Residues in contact with GLN 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 ASN 2.9 18.8 + - - +
240A GLN* 3.9 4.9 - - - +
241A ILE 3.3 0.2 - - - -
242A LEU* 1.3 77.6 - - - +
244A ALA* 1.3 58.5 + - - +
245A ASN* 3.2 4.9 + - - +
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Residues in contact with ALA 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* 3.2 16.6 + - + +
241A ILE* 3.9 4.7 - - - +
242A LEU 3.2 0.8 - - - -
243A GLN* 1.3 75.6 - - - +
245A ASN* 1.3 66.6 + - - +
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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