Contacts of the helix formed by residues 235 - 250 (chain D) in PDB entry 2W3S
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 GLY 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D GLN* 3.5 13.4 + - - -
181D ALA* 5.3 0.7 - - - +
194D CYS* 5.9 1.4 - - - +
195D SER 5.2 3.1 - - - -
196D SER* 5.2 5.6 - - - -
202D ILE* 3.9 15.1 - - - +
231D LYS* 4.6 8.6 + - - +
233D SER* 3.0 3.2 - - - +
234D GLN* 1.3 78.4 - - - +
236D ASN* 1.3 63.5 + - - +
237D HIS 3.2 0.7 + - - -
238D LEU* 3.3 8.3 + - - +
239D ALA* 3.1 22.9 + - - +
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Residues in contact with ASN 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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76D ALA* 2.9 33.3 - - + +
198D HIS 5.4 0.2 + - - -
201D GLU* 3.1 27.2 + - - +
202D ILE* 3.8 28.1 - - - +
205D LYS* 3.6 26.1 - - + +
233D SER* 3.2 19.6 + - - +
235D GLY* 1.3 77.7 - - - +
237D HIS* 1.3 58.0 + - - +
239D ALA* 3.7 1.8 - - - +
240D ILE* 2.9 36.1 + - - +
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Residues in contact with HIS 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 4.0 13.2 - - + -
76D ALA* 3.4 29.0 - - + +
83D GLU* 3.8 20.0 + - - -
84D PRO 4.3 5.9 + - - -
85D VAL* 4.0 31.2 - - + +
97D PRO* 5.2 10.1 - - + -
233D SER 4.4 9.2 + - - -
234D GLN* 3.9 21.5 + - - +
235D GLY 3.2 0.6 - - - -
236D ASN* 1.3 75.6 - - - +
238D LEU* 1.3 62.0 + - + +
240D ILE* 3.5 0.7 + - - -
241D ALA* 3.0 29.3 + - - +
257D TYR* 3.9 17.5 - - - +
265D ILE* 5.6 5.8 - - + +
299D TRP* 5.8 1.8 - - - -
302D ASP* 6.0 0.9 - - - -
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Residues in contact with LEU 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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179D GLN* 3.5 43.5 - - + +
180D ALA* 3.7 9.2 - - - +
181D ALA* 3.7 14.4 - - + -
234D GLN 3.5 22.0 - - - +
235D GLY* 3.3 5.4 + - - +
237D HIS* 1.3 71.9 - - + +
239D ALA* 1.3 67.6 + - - +
241D ALA* 3.2 1.7 + - - +
242D CYS* 2.8 27.5 + - - -
255D MET* 3.8 26.0 - - + +
257D TYR* 3.5 45.5 - - + +
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Residues in contact with ALA 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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181D ALA* 3.7 12.1 - - + +
192D ILE* 4.4 11.1 - - + +
194D CYS* 5.3 0.9 - - + -
202D ILE* 3.7 35.4 - - + -
205D LYS* 6.5 0.4 - - + -
206D VAL* 3.7 10.6 - - + +
235D GLY 3.1 16.8 + - - +
236D ASN* 3.7 3.8 - - - +
238D LEU* 1.3 77.4 - - - +
240D ILE* 1.3 63.2 + - - +
242D CYS* 3.3 3.0 + - - +
243D ALA* 3.0 24.1 + - - +
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Residues in contact with ILE 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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70D LEU* 5.4 6.5 - - + -
73D ASP 5.3 3.6 - - - +
74D ASN* 6.3 0.2 - - - -
75D ASP 4.0 13.5 - - - +
76D ALA* 4.2 3.8 - - - -
85D VAL* 3.9 34.3 - - + -
205D LYS* 3.7 44.2 - - + +
206D VAL* 4.2 5.4 - - + +
209D ALA* 3.6 20.4 - - + +
236D ASN 2.9 28.2 + - - +
237D HIS 4.1 2.2 - - - +
239D ALA* 1.3 70.5 - - - +
241D ALA* 1.3 66.3 + - - +
243D ALA* 3.3 4.5 + - - +
244D VAL* 2.9 30.0 + - + +
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Residues in contact with ALA 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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35D LEU* 3.7 2.9 - - + -
37D PHE* 4.2 7.6 - - + -
85D VAL* 5.2 3.1 - - + -
100D LEU* 3.7 28.1 - - + +
237D HIS 3.0 19.8 + - - +
238D LEU 3.6 2.9 - - - +
240D ILE* 1.3 78.1 - - - +
242D CYS* 1.3 63.1 + - - +
244D VAL* 3.8 2.1 - - - -
245D ALA* 3.0 26.5 + - - +
255D MET* 3.9 20.9 - - - -
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Residues in contact with CYS 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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35D LEU* 3.7 8.5 - - - -
181D ALA* 3.4 19.5 - - + -
182D LEU 4.5 1.6 - - - +
183D ALA* 3.6 18.8 - - + +
192D ILE* 5.6 0.2 - - + -
238D LEU 2.8 22.9 + - - +
239D ALA* 3.8 4.0 - - - +
241D ALA* 1.3 73.0 - - - +
243D ALA* 1.3 53.2 + - - +
246D ALA* 2.8 36.7 + - - +
253D CYS* 3.5 16.4 - - - +
254D LYS 3.7 2.9 - - - -
255D MET* 3.3 37.2 - - - -
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Residues in contact with ALA 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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183D ALA* 3.6 9.1 - - + +
190D VAL* 4.7 3.3 - - + +
192D ILE* 4.2 7.2 - - + -
206D VAL* 3.7 27.6 - - + -
209D ALA* 5.9 0.4 - - + -
210D LEU* 3.4 28.0 - - + +
239D ALA 3.0 17.4 + - - +
240D ILE* 3.7 4.7 - - - +
242D CYS* 1.3 78.7 - - - +
244D VAL* 1.3 56.9 + - - +
246D ALA* 3.9 2.4 - - - +
247D ARG* 3.0 21.5 + - - +
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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
----------------------------------------------------------
65D PHE* 4.2 20.9 - - + -
69D ASP 5.1 0.4 - - - +
70D LEU* 3.8 27.6 - - + -
71D PRO* 4.0 27.6 - - + -
100D LEU* 5.4 3.1 - - + -
209D ALA* 4.2 16.6 - - + +
210D LEU* 4.0 16.8 - - + -
240D ILE* 2.9 22.0 + - + +
241D ALA* 4.0 4.0 - - - +
243D ALA* 1.3 72.6 - - - +
245D ALA* 1.3 61.9 + - - +
247D ARG* 3.3 5.2 + - - +
248D ALA* 2.9 28.2 + - + +
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Residues in contact with ALA 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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35D LEU* 4.0 19.5 - - + -
65D PHE* 3.7 29.6 - - + -
100D LEU* 4.5 2.4 - - + +
102D ALA* 4.5 3.1 - - + -
241D ALA 3.0 15.9 + - - +
244D VAL* 1.3 77.4 - - - +
246D ALA* 1.3 58.2 + - - +
249D THR* 2.8 35.4 + - + +
253D CYS* 3.5 17.9 - - - -
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Residues in contact with ALA 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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183D ALA* 4.0 15.0 - - + +
185D PRO* 4.0 23.2 - - + +
190D VAL* 5.8 2.9 - - + -
242D CYS 2.8 23.5 + - - +
243D ALA* 3.9 3.8 - - - +
244D VAL 3.2 0.2 - - - -
245D ALA* 1.3 72.9 - - - +
247D ARG* 1.3 54.7 + - - +
250D GLY* 2.7 36.6 + - - -
251D ARG 3.3 22.6 + - - +
253D CYS* 3.4 3.9 - - - -
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Residues in contact with ARG 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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71D PRO* 3.3 38.4 - - - +
72D HIS* 5.0 5.3 - - - -
185D PRO* 5.9 2.2 - - - -
190D VAL* 6.1 1.7 - - + +
210D LEU* 4.1 35.2 + - + -
243D ALA 3.0 19.3 + - - +
244D VAL* 3.6 5.0 + - - +
246D ALA* 1.3 76.8 - - - +
248D ALA* 1.3 76.7 + - - +
250D GLY* 3.5 7.1 + - - -
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Residues in contact with ALA 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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65D PHE* 3.4 33.2 - - + -
244D VAL* 2.9 17.0 + - + +
245D ALA 3.7 0.4 - - - +
247D ARG* 1.3 87.8 - - - +
249D THR* 1.3 59.9 + - + +
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Residues in contact with THR 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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33D LEU* 3.6 27.1 - - + +
62D ILE* 4.2 9.6 - - + -
63D ALA* 4.0 27.1 - - + -
65D PHE* 4.8 1.1 - - + -
102D ALA* 5.0 2.9 - - + -
245D ALA* 2.8 28.5 + - - +
248D ALA* 1.3 75.7 - - + +
250D GLY* 1.3 60.8 + - - +
251D ARG* 3.1 32.7 + - - +
253D CYS* 4.0 0.2 - - - -
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Residues in contact with GLY 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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31D ASN* 5.4 1.2 + - - -
185D PRO* 4.0 15.2 - - - +
246D ALA 2.7 15.4 + - - -
247D ARG 3.5 5.4 + - - -
248D ALA 3.4 2.6 - - - -
249D THR* 1.3 76.4 - - - +
251D ARG* 1.3 57.5 + - - +
252D PRO* 4.6 0.9 - - - +
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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