Contacts of the helix formed by residues 242 - 258 (chain A) in PDB entry 1TQN
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A LYS* 4.8 19.1 - - + +
210A LEU* 5.1 7.2 - - + -
213A PHE* 5.9 1.3 - - + -
239A CYS 5.0 1.1 - - - +
240A VAL 3.6 6.9 - - - +
241A PHE* 1.3 82.0 - - + +
243A ARG* 1.3 53.8 + - - +
244A GLU* 3.0 7.4 - - + +
245A VAL* 2.8 30.3 + - + +
246A THR* 2.7 34.1 + - + +
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Residues in contact with ARG 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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236A LEU 5.1 2.0 + - - -
237A ASN* 3.5 47.6 + - - +
238A ILE* 4.9 6.3 - - - +
239A CYS* 5.4 6.7 + - + +
241A PHE 3.0 7.6 + - - +
242A PRO* 1.3 70.9 - - - +
244A GLU* 1.3 58.3 + - - +
246A THR* 2.9 12.6 - - - +
247A ASN* 2.6 66.9 + - - +
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Residues in contact with GLU 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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206A ASN* 4.3 5.3 - - - +
209A LYS* 3.7 27.1 + - - +
242A PRO* 4.5 9.9 - - + -
243A ARG* 1.3 80.1 - - - +
245A VAL* 1.3 59.7 + - + +
247A ASN* 4.1 4.4 - - - +
248A PHE* 3.6 18.2 + - - +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASN* 3.5 36.3 - - + +
209A LYS* 3.4 39.3 - - + +
210A LEU* 4.2 17.7 - - + -
242A PRO* 2.8 21.0 + - + +
244A GLU* 1.3 76.4 - - + +
246A THR* 1.3 65.0 + - + +
247A ASN 3.2 1.3 - - - -
248A PHE* 3.3 5.7 + - - +
249A LEU* 3.1 39.9 + - + +
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Residues in contact with THR 246 (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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113A PHE* 4.0 23.3 - - + -
114A MET* 5.1 2.7 - - + -
210A LEU* 5.6 2.5 - - + -
239A CYS* 5.7 1.6 - - - -
241A PHE* 3.6 29.6 - - + +
242A PRO* 2.7 22.5 + - + +
243A ARG* 2.9 27.2 - - - +
245A VAL* 1.3 75.8 - - + +
247A ASN* 1.3 63.3 + - - +
249A LEU* 3.7 0.9 + - - +
250A ARG* 3.0 28.7 + - - +
300A ILE* 4.2 23.4 - - + +
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Residues in contact with ASN 247 (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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243A ARG* 2.6 52.6 + - - +
244A GLU* 4.1 4.9 - - - +
246A THR* 1.3 74.0 + - - +
248A PHE* 1.3 65.6 + - - +
250A ARG* 2.9 35.9 + - - +
251A LYS* 3.0 26.5 + - + +
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Residues in contact with PHE 248 (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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202A PRO* 5.0 4.0 - - + -
203A PHE* 3.4 58.6 - + + -
206A ASN* 3.4 36.3 - - + -
244A GLU 3.6 13.2 + - - +
245A VAL 3.3 7.2 + - - +
247A ASN* 1.3 80.7 - - - +
249A LEU* 1.3 74.2 + - + +
251A LYS* 3.2 6.2 + - + +
252A SER* 2.8 40.9 + - - -
255A ARG* 6.2 0.7 - - - -
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Residues in contact with LEU 249 (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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203A PHE* 3.9 12.6 - - + -
207A THR* 3.7 21.5 - - + +
210A LEU* 3.9 24.0 - - + -
245A VAL* 3.1 23.0 + - + +
246A THR 4.3 2.5 - - - +
248A PHE* 1.3 97.9 - - + +
250A ARG* 1.3 60.6 + - - +
252A SER* 3.9 4.3 - - - -
253A VAL* 2.8 42.5 + - + +
296A VAL* 4.6 0.7 - - - -
300A ILE* 3.7 31.0 - - + -
303A ILE* 4.4 10.3 - - + -
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Residues in contact with ARG 250 (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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113A PHE* 3.7 39.8 - - - +
246A THR 3.0 16.9 + - - +
247A ASN* 2.9 25.2 + - - +
249A LEU* 1.3 75.9 - - - +
251A LYS* 1.3 82.6 + - - +
253A VAL* 4.0 2.6 - - - +
254A LYS* 3.3 21.8 + - - +
293A LEU* 2.9 42.6 - - + +
296A VAL* 3.6 24.2 - - + +
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Residues in contact with LYS 251 (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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247A ASN* 3.0 26.4 + - + +
248A PHE* 3.6 8.7 - - + +
250A ARG* 1.3 105.8 + - - +
252A SER* 1.3 65.2 + - - +
254A LYS* 3.1 29.4 + - + +
255A ARG* 3.2 11.2 + - - +
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Residues in contact with SER 252 (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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203A PHE* 4.1 18.5 - - - -
248A PHE* 2.8 45.4 + - - -
249A LEU* 3.2 9.6 + - - -
251A LYS* 1.3 77.4 - - - +
253A VAL* 1.3 59.7 + - - +
255A ARG* 3.2 29.0 + - - +
256A MET* 3.0 26.9 - - - +
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Residues in contact with VAL 253 (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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249A LEU* 2.8 28.0 + - + +
250A ARG 4.0 4.3 - - - +
252A SER* 1.3 74.8 - - - +
254A LYS* 1.3 54.4 + - - +
256A MET* 3.5 9.5 - - + +
257A LYS* 2.7 49.4 + - + +
272A LEU* 3.9 21.1 - - + -
295A LEU* 3.8 26.9 - - + -
296A VAL* 4.2 19.1 - - + -
299A SER* 4.7 15.9 - - - +
300A ILE* 6.5 0.2 - - + -
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Residues in contact with LYS 254 (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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250A ARG 3.3 13.6 + - - +
251A LYS* 3.1 23.3 + - + +
253A VAL* 1.3 82.5 - - - +
255A ARG* 1.3 59.6 + - - +
257A LYS* 3.4 10.7 + - - +
258A GLU* 2.9 44.7 + - + +
292A ASP* 4.8 17.9 + - + -
296A VAL* 5.6 1.3 - - + +
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Residues in contact with ARG 255 (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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203A PHE* 5.8 5.3 - - - +
248A PHE* 6.2 1.2 - - - -
251A LYS 3.2 7.8 + - - +
252A SER* 3.2 26.3 + - - +
254A LYS* 1.3 75.6 - - - +
256A MET* 1.3 71.7 + - - +
257A LYS 3.0 1.1 - - - -
258A GLU* 2.6 12.2 + - - -
259A SER* 2.5 47.6 + - - +
260A ARG* 4.5 18.2 - - - +
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Residues in contact with MET 256 (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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188A SER 4.7 2.7 - - - +
189A PHE* 3.5 25.8 - - + -
191A VAL* 4.2 13.7 - - + -
203A PHE* 4.6 9.4 - - + -
252A SER* 3.0 34.8 - - - +
253A VAL* 3.5 11.7 - - + +
255A ARG* 1.3 86.2 - - + +
257A LYS* 1.3 64.0 + - - +
258A GLU 3.2 1.0 + - - +
259A SER* 4.2 0.2 - - - -
260A ARG* 3.2 74.8 + - - +
261A LEU 3.9 0.7 + - - -
272A LEU* 3.3 28.0 - - + -
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Residues in contact with LYS 257 (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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253A VAL* 2.7 34.5 + - + +
254A LYS* 3.4 16.6 - - - +
255A ARG 3.0 0.2 + - - -
256A MET* 1.3 74.8 - - - +
258A GLU* 1.3 73.1 + - - +
261A LEU* 5.1 2.4 - - - +
262A GLU* 3.5 12.0 + - - +
276A ILE* 3.3 42.3 - - + +
279A GLN* 2.5 47.7 + - - +
292A ASP* 3.5 22.5 + - + +
295A LEU* 3.2 15.3 - - + +
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Residues in contact with GLU 258 (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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254A LYS* 2.9 41.4 + - + +
255A ARG* 2.6 10.6 + - - +
257A LYS* 1.3 88.2 - - - +
259A SER* 1.3 58.1 - - - +
260A ARG 2.6 18.1 + - - -
261A LEU 3.5 0.7 + - - -
262A GLU* 2.8 50.7 + - + +
292A ASP* 5.4 1.7 - - - +
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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