Contacts of the helix formed by residues 241 - 251 (chain D) in PDB entry 1KQN
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 PRO 241 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C TYR* 5.5 3.4 - - + -
20D ILE* 5.0 0.9 - - + +
21D THR* 4.5 4.0 - - - -
22D ASN* 3.4 15.5 - - - +
25D LEU* 3.6 28.5 - - + -
72D LEU 5.3 2.0 - - - +
73D ALA* 4.0 20.6 - - + +
240D VAL* 1.3 89.9 - - + +
242D ASP* 1.3 67.4 + - - +
243D LEU* 4.5 2.5 - - + +
244D VAL* 2.8 33.8 + - + +
245D GLN 2.9 9.9 + - - -
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Residues in contact with ASP 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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76C ASN* 4.7 7.6 - - - +
237D ARG* 3.0 42.5 + - - +
238D TYR* 5.1 7.4 + - - -
240D VAL 3.3 4.1 + - - +
241D PRO* 1.3 70.2 - - - +
243D LEU* 1.3 59.2 + - + +
245D GLN* 3.2 9.1 + - - +
246D GLU* 2.8 49.4 + - - +
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Residues in contact with LEU 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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72D LEU* 3.8 45.5 - - + +
75D LYS* 3.9 29.8 - - + +
76D ASN* 5.5 6.7 - - - +
241D PRO* 3.2 3.6 - - + +
242D ASP* 1.3 76.6 - - + +
244D VAL* 1.3 62.3 + - - +
246D GLU* 3.7 20.7 - - + +
247D TYR* 2.9 28.2 + - - +
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Residues in contact with VAL 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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20D ILE* 4.0 18.8 - - + +
69D MET* 3.3 44.0 - - + +
72D LEU* 4.3 3.1 - - + -
73D ALA* 3.8 23.6 - - + +
240D VAL* 4.4 6.3 - - + -
241D PRO* 2.8 21.9 + - + +
243D LEU* 1.3 74.3 - - - +
245D GLN* 1.3 67.5 + - - +
247D TYR* 3.1 7.2 + - - +
248D ILE* 2.8 42.1 + - + +
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Residues in contact with GLN 245 (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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235D SER* 5.1 0.8 + - - -
236D ILE* 4.0 24.1 - - + +
237D ARG* 3.6 46.9 + - - +
240D VAL* 3.7 18.4 - - + +
241D PRO 2.9 6.8 + - - +
242D ASP* 3.3 13.7 - - - +
244D VAL* 1.3 78.4 - - - +
246D GLU* 1.3 65.6 + - - +
248D ILE* 3.3 7.6 + - - +
249D GLU* 2.9 58.5 + - + +
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Residues in contact with GLU 246 (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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237D ARG* 5.5 1.0 + - - -
242D ASP* 2.8 41.4 + - - +
243D LEU* 3.7 25.6 - - + +
245D GLN* 1.3 81.4 - - - +
247D TYR* 1.3 66.0 + - - +
249D GLU* 3.4 11.7 + - - +
250D LYS* 2.9 25.5 + - - +
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Residues in contact with TYR 247 (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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64D TYR* 4.6 2.3 - - - -
65D HIS* 2.8 41.1 + + - -
68D ILE* 3.6 35.2 - - + +
69D MET* 3.5 24.0 - - + -
72D LEU* 3.8 21.1 - - + -
243D LEU 2.9 18.8 + - - +
244D VAL* 3.1 5.4 + - - +
246D GLU* 1.3 76.3 - - - +
248D ILE* 1.3 62.8 + - - +
250D LYS* 3.3 5.6 + - + +
251D HIS* 3.0 56.4 + + - +
253D LEU* 3.7 12.1 - - + -
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Residues in contact with ILE 248 (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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19D PRO* 4.1 19.7 - - + -
69D MET* 3.6 22.7 - - - -
230D LEU* 4.0 30.5 - - + -
236D ILE* 4.3 18.4 - - + -
240D VAL* 5.3 0.4 - - + -
244D VAL* 2.8 34.0 + - + +
245D GLN* 3.6 7.4 - - - +
247D TYR* 1.3 76.1 - - - +
249D GLU* 1.3 60.9 + - + +
252D ASN* 2.9 24.5 + - - -
253D LEU* 3.2 27.0 + - + +
254D TYR* 4.3 7.2 - - + +
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Residues in contact with GLU 249 (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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230D LEU* 6.1 2.7 - - + -
236D ILE* 5.6 0.6 - - + +
245D GLN* 2.9 51.2 + - + +
246D GLU* 3.8 10.6 - - - +
247D TYR 3.3 0.2 - - - -
248D ILE* 1.3 77.2 - - + +
250D LYS* 1.3 67.0 + - - +
252D ASN* 3.3 22.3 + - - +
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Residues in contact with LYS 250 (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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246D GLU 2.9 18.1 + - - +
247D TYR* 3.8 6.3 - - + +
249D GLU* 1.3 78.3 - - - +
251D HIS* 1.3 83.1 + - + +
252D ASN* 4.8 3.5 + - - -
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Residues in contact with HIS 251 (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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65D HIS* 4.5 8.1 + - - +
247D TYR* 3.0 65.8 + + - +
250D LYS* 1.3 99.3 + - + +
252D ASN* 1.3 70.2 + - - +
253D LEU* 3.0 24.2 + - + +
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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