Contacts of the helix formed by residues 241 - 252 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A TYR* 5.6 3.1 - - + -
20B ILE* 4.9 1.6 - - + +
21B THR* 4.6 3.4 - - - -
22B ASN* 3.4 13.9 - - - +
25B LEU* 3.7 27.1 - - + -
72B LEU 5.4 0.4 - - - +
73B ALA* 4.0 22.4 - - + +
240B VAL* 1.3 89.1 - - + +
242B ASP* 1.3 67.6 + - - +
243B LEU* 4.5 4.7 - - + +
244B VAL* 2.8 32.3 + - + +
245B GLN 2.9 9.9 + - - -
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Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN* 5.4 4.5 - - - +
237B ARG* 3.0 40.5 + - - -
238B TYR* 5.4 3.6 + - - -
240B VAL 3.5 3.8 + - - +
241B PRO* 1.3 70.3 - - - +
243B LEU* 1.3 58.5 + - + +
245B GLN* 3.2 8.5 + - - +
246B GLU* 2.8 52.0 + - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.6 49.9 - - + +
75B LYS* 4.0 28.0 - - + +
76B ASN* 4.4 12.3 - - - +
241B PRO* 3.0 4.7 + - + +
242B ASP* 1.3 80.3 - - + +
244B VAL* 1.3 59.2 + - - +
246B GLU* 3.5 16.2 + - + +
247B TYR* 3.0 27.5 + - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO* 4.9 0.2 - - + -
20B ILE* 4.0 18.8 - - + +
69B MET* 3.4 42.4 - - + +
72B LEU* 4.5 2.7 - - + -
73B ALA* 3.8 22.0 - - + +
240B VAL* 4.3 5.2 - - + -
241B PRO* 2.8 23.1 + - + +
243B LEU* 1.3 73.2 - - - +
245B GLN* 1.3 62.1 + - - +
247B TYR* 3.1 7.2 + - - +
248B ILE* 2.8 48.8 + - + +
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Residues in contact with GLN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B SER* 5.1 0.6 + - - +
236B ILE* 4.3 18.2 - - + +
237B ARG* 3.6 50.5 - - - +
240B VAL* 3.8 19.9 - - + +
241B PRO 2.9 7.4 + - - +
242B ASP* 3.4 10.6 - - - +
244B VAL* 1.3 79.4 - - - +
246B GLU* 1.3 71.3 + - - +
248B ILE* 3.3 7.6 + - - +
249B GLU* 3.0 53.4 + - + +
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ARG* 5.6 0.9 + - - -
242B ASP* 2.8 40.7 + - - +
243B LEU* 3.7 17.3 + - + +
245B GLN* 1.3 91.3 - - - +
247B TYR* 1.3 56.3 + - - +
249B GLU* 3.4 13.3 + - - +
250B LYS* 2.8 29.4 + - - +
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Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TYR* 4.6 0.9 - - - -
65B HIS* 2.7 41.7 + + - -
68B ILE* 3.5 35.9 - - + +
69B MET* 3.4 25.6 - - + -
72B LEU* 3.8 20.4 - - + -
243B LEU 3.0 14.5 + - - +
244B VAL* 3.5 8.7 - - - +
246B GLU* 1.3 74.3 - - - +
248B ILE* 1.3 66.8 + - - +
250B LYS* 3.0 7.2 + - + -
251B HIS* 3.0 58.7 + + - -
253B LEU* 3.7 12.3 - - + -
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PRO* 4.2 18.8 - - + -
69B MET* 3.6 21.3 - - - -
230B LEU* 3.9 34.3 - - + -
236B ILE* 4.3 19.3 - - + -
240B VAL* 5.1 0.7 - - + -
244B VAL* 2.8 41.0 + - + +
245B GLN* 3.6 5.2 - - - +
247B TYR* 1.3 73.1 - - - +
249B GLU* 1.3 59.9 + - + +
252B ASN* 2.9 24.3 + - - -
253B LEU* 3.1 28.5 + - + +
254B TYR* 4.3 5.2 - - + +
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU* 5.9 4.5 - - + -
236B ILE* 5.9 0.3 - - - +
245B GLN* 3.0 51.9 + - + +
246B GLU* 3.7 12.1 - - - +
248B ILE* 1.3 79.1 - - + +
250B LYS* 1.3 65.8 + - - +
252B ASN* 3.2 21.4 + - - +
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B GLU 2.8 21.5 + - - +
247B TYR* 3.0 4.7 + - + +
249B GLU* 1.3 74.4 - - - +
251B HIS* 1.3 86.3 + - + +
252B ASN* 3.8 3.3 + - - -
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Residues in contact with HIS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 3.8 16.1 + - + +
247B TYR* 3.0 52.5 + + - +
250B LYS* 1.3 106.5 + - + +
252B ASN* 1.3 71.1 + - - +
253B LEU* 3.2 22.7 + - + +
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Residues in contact with ASN 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ILE* 2.9 9.3 + - - -
249B GLU* 3.2 15.7 + - - +
250B LYS 3.5 3.0 + - - -
251B HIS* 1.3 77.9 - - - +
253B LEU* 1.3 63.9 + - - +
254B TYR* 3.4 6.7 + - - +
255B SER* 5.5 2.6 - - - -
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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