Contacts of the helix formed by residues 234 - 244 (chain D) in PDB entry 3K9X
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 234 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D HIS* 3.8 21.1 - + - -
101D PHE* 3.5 40.6 - + - -
103D ILE* 3.5 28.0 - - + -
179D ASN* 3.6 34.8 - - + -
229D THR* 3.7 28.3 - - + -
230D LYS 3.4 22.2 - - - -
231D VAL 2.8 9.1 + - - +
233D ALA* 1.3 86.9 - - + +
235D LEU* 1.3 59.4 + - - +
236D LYS 3.3 2.9 - - - -
237D TRP* 3.1 11.1 + - + -
238D ILE* 2.7 33.6 + - + +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GOL 3.9 15.6 + - - +
123D LEU* 4.2 14.0 - - + +
124D PRO* 3.4 45.1 - - + +
125D ARG* 3.5 32.5 - - + +
231D VAL* 3.4 31.2 - - + +
232D THR* 3.6 26.8 + - + +
233D ALA 3.7 0.6 - - - -
234D PHE* 1.3 78.1 - - - +
236D LYS* 1.3 58.5 + - - +
238D ILE* 3.4 5.1 + - + +
239D ASP* 2.9 30.1 + - - +
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Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ALA 5.9 1.3 - - - +
234D PHE 3.3 0.2 - - - -
235D LEU* 1.3 76.5 - - - +
237D TRP* 1.3 65.3 + - - +
239D ASP* 3.2 7.3 + - + +
240D ARG* 3.0 49.6 + - + +
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Residues in contact with TRP 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE* 3.6 29.2 - - + -
90D LYS 4.0 1.8 - - - -
91D HIS* 3.3 64.5 + + + +
92D ASN* 5.1 3.4 + - - +
103D ILE* 3.8 25.4 - - + -
104D ALA* 4.1 2.9 - - - -
105D VAL* 3.9 21.1 - - + -
233D ALA 5.5 0.4 + - - +
234D PHE* 3.1 16.1 + - + +
236D LYS* 1.3 80.8 - - - +
238D ILE* 1.3 71.2 + - + +
240D ARG* 3.3 35.9 + - - +
241D SER* 2.9 43.7 + - - -
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Residues in contact with ILE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.9 9.6 - - + -
53D LEU* 4.2 13.7 - - + -
103D ILE* 4.0 17.7 - - + -
105D VAL* 4.5 3.4 - - + -
123D LEU* 3.6 37.0 - - + -
231D VAL* 4.2 22.0 - - + -
234D PHE* 2.7 30.7 + - + +
235D LEU* 3.7 6.7 - - - +
237D TRP* 1.3 89.6 - - + +
239D ASP* 1.3 64.2 + - - +
241D SER* 3.1 5.8 + - - -
242D MET* 3.0 34.5 + - + +
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Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GOL 4.4 23.0 + - - +
123D LEU* 6.0 1.5 - - + +
235D LEU 2.9 18.5 + - - +
236D LYS* 3.7 7.4 - - - +
238D ILE* 1.3 79.2 - - - +
240D ARG* 1.3 61.4 + - - +
242D MET* 3.3 7.3 + - - +
243D LYS* 3.2 42.2 + - - +
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Residues in contact with ARG 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 4.2 11.2 - - + +
236D LYS* 3.0 51.2 + - + +
237D TRP* 3.4 40.1 - - + +
238D ILE 3.3 0.2 - - - -
239D ASP* 1.3 78.0 - - + +
241D SER* 1.3 61.5 + - - +
242D MET 3.4 0.3 + - - -
243D LYS* 3.5 10.3 + - - +
244D THR* 3.3 15.8 + - - -
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Residues in contact with SER 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 5.6 1.6 - - - -
51D TYR* 3.5 16.3 + - - -
89D ILE* 4.1 30.3 - - - +
105D VAL* 4.4 14.8 - - - -
237D TRP* 2.9 39.5 + - - -
238D ILE 3.1 7.1 + - - -
240D ARG* 1.3 76.7 - - - +
242D MET* 1.3 62.3 + - - +
244D THR* 3.4 16.1 + - - -
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Residues in contact with MET 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ARG* 3.8 21.1 - - - +
47D LEU* 3.9 26.0 - - + +
48D SER* 3.8 25.8 - - - +
51D TYR* 3.5 42.7 + - + -
105D VAL* 4.9 4.5 - - + -
123D LEU* 4.0 11.7 - - + -
238D ILE* 3.0 35.9 + - + +
239D ASP* 3.9 7.9 - - - +
240D ARG 3.1 0.4 - - - -
241D SER* 1.3 77.1 - - - +
243D LYS* 1.3 63.8 + - + +
245D ARG* 3.8 6.9 + - - +
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ASP* 3.2 37.4 + - - +
240D ARG* 3.5 6.3 + - - +
241D SER 3.3 0.4 - - - -
242D MET* 1.3 76.0 - - + +
244D THR* 1.3 70.1 + - - +
245D ARG* 3.0 17.6 + - - +
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Residues in contact with THR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B THR* 4.1 13.0 - - - +
133B GLN 4.0 20.2 - - - +
134B LYS* 3.2 31.0 - - + +
162B TYR* 4.7 15.5 - - + +
164B ASP* 4.7 3.6 + - - +
51D TYR* 4.7 1.1 - - - -
89D ILE* 5.7 0.9 - - - +
240D ARG 3.3 9.8 + - - -
241D SER* 3.4 12.3 + - - -
243D LYS* 1.3 79.9 - - - +
245D ARG* 1.3 72.2 + - - +
246D GLY 3.9 6.9 - - - +
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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