Contacts of the helix formed by residues 241 - 258 (chain A) in PDB entry 1W3U
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PHE* 5.0 8.7 - - + +
73A ILE 5.3 0.2 - - - +
74A GLN* 3.7 28.0 - - + +
203A GLY* 3.4 29.2 - - - +
204A VAL* 4.1 14.8 - - + -
240A PRO* 1.3 84.6 - - + +
242A SER* 1.3 59.4 + - - +
243A PHE 3.4 2.0 - - - -
244A GLY* 3.1 6.9 + - - +
245A ILE* 2.9 37.8 + - + +
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Residues in contact with SER 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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37A ILE* 4.6 11.2 + - - -
38A MET* 5.0 6.9 + - - -
40A MET 5.1 6.3 + - - -
42A HIS* 5.3 3.4 - - - -
47A TYR* 3.3 44.2 - - - -
239A THR* 5.7 2.3 - - - +
240A PRO* 2.9 16.1 + - - -
241A PRO* 1.3 69.1 - - - +
243A PHE* 1.3 70.2 + - - +
245A ILE 3.2 0.5 + - - -
246A TYR* 2.9 23.6 + - - +
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Residues in contact with PHE 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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23A ALA* 4.8 3.4 - - + -
27A PHE* 3.6 35.9 - + - -
37A ILE* 3.5 25.6 - - + -
38A MET* 3.6 28.3 - - + +
241A PRO 3.4 0.2 - - - -
242A SER* 1.3 83.7 + - - +
244A GLY* 1.3 59.1 + - - +
246A TYR* 3.3 23.4 + + - +
247A MET* 2.9 58.6 + - + +
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Residues in contact with GLY 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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201A PRO* 3.4 31.1 - - - +
202A SER 5.3 3.4 - - - -
203A GLY 5.9 0.2 - - - -
204A VAL* 4.3 9.0 - - - -
241A PRO* 3.1 11.4 + - - +
243A PHE* 1.3 79.8 - - - +
245A ILE* 1.3 57.6 + - - +
247A MET* 3.2 1.5 + - - -
248A VAL* 2.9 26.0 + - - +
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Residues in contact with ILE 245 (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 TYR* 3.2 31.9 - - + +
50A VAL* 4.5 0.7 - - - +
51A HIS* 3.8 20.0 - - + +
54A ALA* 4.3 4.2 - - + +
72A PHE* 3.5 60.1 - - + -
204A VAL* 4.0 11.7 - - + -
240A PRO* 3.8 15.0 - - + -
241A PRO* 2.9 22.1 + - + +
242A SER 3.2 0.4 + - - +
244A GLY* 1.3 73.2 - - - +
246A TYR* 1.3 61.4 + - - +
248A VAL* 3.2 7.2 + - - +
249A ASN* 2.9 28.4 + - - +
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Residues in contact with TYR 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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23A ALA* 3.3 18.6 + - + -
26A GLU* 2.5 42.6 + - + +
30A TYR* 3.8 17.0 - + - -
37A ILE* 4.0 26.2 - - + -
47A TYR* 5.2 0.2 - - + -
50A VAL* 3.6 25.7 - - + +
242A SER 2.9 13.3 + - - +
243A PHE* 3.5 39.3 - + - +
245A ILE* 1.3 78.1 - - - +
247A MET* 1.3 74.7 + - - +
249A ASN* 3.2 5.3 + - + +
250A GLU* 3.0 47.8 + - + +
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Residues in contact with MET 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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15A LEU* 3.6 28.7 - - + -
19A VAL* 3.8 20.1 - - + +
20A LEU* 4.7 8.7 - - + -
23A ALA* 3.6 29.2 - - + -
201A PRO* 3.8 23.3 - - + -
243A PHE* 2.9 42.2 + - + +
244A GLY 3.2 6.0 + - - +
246A TYR* 1.3 84.7 - - + +
248A VAL* 1.3 66.8 + - - +
250A GLU* 3.1 5.8 + - - +
251A VAL* 2.9 25.7 + - - +
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Residues in contact with VAL 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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54A ALA* 4.8 1.6 - - + -
58A LEU* 5.1 2.2 - - + -
72A PHE* 4.7 15.5 - - + -
195A ALA* 4.1 7.6 - - + -
199A LEU* 3.7 26.2 - - + +
201A PRO* 4.1 4.7 - - + +
204A VAL* 3.8 25.8 - - + -
206A VAL* 4.9 8.5 - - + -
244A GLY 2.9 19.4 + - - +
245A ILE* 3.5 9.9 - - - +
247A MET* 1.3 77.1 - - - +
249A ASN* 1.3 57.9 + - - +
251A VAL* 3.1 2.8 + - - +
252A LEU* 2.8 50.1 + - + +
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Residues in contact with ASN 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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50A VAL* 4.0 21.0 - - + +
53A GLU* 3.1 31.3 + - - +
54A ALA* 3.2 29.3 + - + +
57A ARG* 3.2 24.6 - - - -
245A ILE 2.9 15.8 + - - +
246A TYR* 3.2 9.1 + - - +
248A VAL* 1.3 72.5 - - - +
250A GLU* 1.3 66.6 + - - +
252A LEU* 3.2 4.3 + - - +
253A LYS* 2.9 41.2 + - - +
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Residues in contact with GLU 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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19A VAL* 3.7 25.0 - - + +
22A ARG* 3.8 28.9 + - + +
23A ALA* 5.3 2.5 - - + -
26A GLU* 4.5 5.7 - - - +
246A TYR* 3.0 50.4 + - + +
247A MET* 3.1 9.6 + - - +
249A ASN* 1.3 80.4 + - - +
251A VAL* 1.3 60.3 + - - +
253A LYS* 2.9 42.1 + - - +
254A TRP* 3.0 21.3 + - - +
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Residues in contact with VAL 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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15A LEU* 4.5 3.4 - - + -
16A PRO* 4.3 14.6 - - + -
19A VAL* 4.1 21.8 - - + -
198A ASN 4.3 4.9 - - - +
199A LEU* 3.2 45.1 - - + +
200A GLY* 4.0 7.9 - - - -
247A MET 2.9 14.5 + - - +
248A VAL 3.6 2.9 - - - +
250A GLU* 1.3 71.7 - - - +
252A LEU* 1.4 63.1 + - + +
254A TRP* 3.0 12.9 + - + +
255A ILE* 2.8 40.6 + - + +
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Residues in contact with LEU 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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54A ALA* 3.3 36.8 - - + +
57A ARG* 4.0 17.3 + - + +
58A LEU* 3.9 17.0 - - + +
61A LEU* 3.7 16.3 - - + +
179A LEU* 3.4 33.2 - - + -
199A LEU* 4.7 3.6 - - + -
248A VAL* 2.8 41.3 + - + +
249A ASN 3.2 4.0 + - - +
251A VAL* 1.4 72.2 - - + +
253A LYS* 1.3 63.8 + - - +
255A ILE* 3.2 10.1 + - + +
256A GLU* 3.0 23.2 + - - +
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Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 4.8 10.5 - - - +
53A GLU* 3.7 12.6 + - - -
57A ARG* 3.3 35.0 - - - +
249A ASN* 2.9 33.6 + - - +
250A GLU* 2.9 41.3 + - - +
251A VAL 3.2 0.2 - - - -
252A LEU* 1.3 75.9 - - - +
254A TRP* 1.3 63.1 + - - +
256A GLU* 3.2 5.1 + - - +
257A GLU* 2.9 28.9 + - + +
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Residues in contact with TRP 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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16A PRO* 3.3 38.3 - - + +
18A GLU* 3.3 22.9 - - + +
19A VAL* 3.7 11.2 - - + -
22A ARG* 4.8 1.1 - - - +
250A GLU 3.0 12.6 + - - +
251A VAL* 3.0 12.4 + - + +
253A LYS* 1.3 78.6 - - - +
255A ILE* 1.3 89.6 + - + +
257A GLU* 3.0 11.7 + - - +
258A ARG* 2.9 76.1 + - + +
264A VAL* 4.7 5.2 - - + -
340A ASN* 3.6 45.8 - - + -
341A ALA* 3.9 8.5 - - + -
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Residues in contact with ILE 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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61A LEU* 3.7 22.0 - - + -
179A LEU* 3.9 29.6 - - + -
198A ASN 4.8 0.2 - - - +
199A LEU* 4.6 3.6 - - + -
251A VAL* 2.8 33.9 + - + +
252A LEU* 3.2 11.0 + - + +
254A TRP* 1.3 91.4 - - + +
256A GLU* 1.3 65.0 + - - +
258A ARG* 3.0 12.4 + - - +
259A GLY 3.3 0.9 + - - -
260A GLY 2.9 25.2 + - - +
261A LEU* 4.0 12.1 - - + -
264A VAL* 4.3 7.9 - - + -
340A ASN* 3.8 19.3 - - - +
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Residues in contact with GLU 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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57A ARG* 3.2 24.5 + - - +
61A LEU* 4.4 11.9 - - + +
252A LEU 3.0 12.0 + - - +
253A LYS* 3.6 7.9 - - - +
254A TRP 3.2 0.4 - - - -
255A ILE* 1.3 78.4 - - - +
257A GLU* 1.3 62.2 + - - +
259A GLY* 2.9 13.9 + - - -
260A GLY* 3.4 11.5 + - - +
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Residues in contact with GLU 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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18A GLU* 2.6 26.3 - - - +
22A ARG* 2.8 36.4 + - - -
253A LYS* 2.9 21.8 + - - +
254A TRP* 3.3 8.7 - - - +
256A GLU* 1.3 75.7 - - - +
258A ARG* 1.3 85.3 + - - +
259A GLY* 3.1 1.1 + - - -
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Residues in contact with ARG 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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18A GLU* 3.9 4.6 + - - -
254A TRP* 2.9 80.2 + - + +
255A ILE 3.0 8.0 + - - +
257A GLU* 1.3 113.0 + - - +
259A GLY* 1.3 58.8 + - - +
260A GLY 3.6 0.7 - - - -
263A GLY* 3.8 16.0 - - - -
264A VAL* 3.9 15.5 - - + -
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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