Contacts of the helix formed by residues 233 - 250 (chain A) in PDB entry 1HMU
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 SER 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLN* 2.8 24.4 + - - -
232A SER* 1.3 82.6 + - - +
234A TYR* 1.3 80.1 + - - -
236A ALA* 2.9 15.2 + - - +
237A VAL* 3.2 12.8 + - - +
285A VAL 4.0 0.9 - - - -
286A GLU* 3.3 34.0 + - - -
287A GLY* 4.3 1.0 - - - -
288A ARG 5.1 0.9 + - - -
289A GLY* 5.3 0.5 + - - -
292A ARG* 5.7 1.5 + - - +
1D ASG 3.7 18.4 + - - +
2D GCD 4.8 1.4 + - - -
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Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TRP* 6.2 0.4 - - - -
174A ALA* 3.7 18.0 - - + +
175A ASN* 4.5 14.1 - - - -
222A TYR* 3.9 3.4 - - + -
224A GLN* 3.3 41.3 - - + +
225A HIS* 3.0 42.6 + + - -
230A GLN* 3.6 28.0 - - + +
232A SER 3.0 0.2 + - - -
233A SER* 1.3 85.1 + - - +
235A GLY* 1.3 57.8 + - - +
237A VAL* 2.9 7.5 + - + +
238A PHE* 2.8 28.4 + - - +
288A ARG* 3.1 19.4 + - - -
371A GLU* 4.6 0.2 - - - -
1D ASG 3.2 39.8 + - + +
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Residues in contact with GLY 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 3.4 19.4 - - - -
230A GLN 2.9 19.8 + - - -
231A ILE 3.6 9.9 - - - -
232A SER 2.8 11.4 + - - -
234A TYR* 1.3 73.3 - - - +
236A ALA* 1.3 55.9 + - - +
238A PHE* 3.3 6.1 - - - +
239A ILE* 3.0 31.8 + - - +
267A TYR* 3.9 2.5 - - - -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ILE 3.9 0.4 + - - -
232A SER* 3.5 15.0 + - - +
233A SER* 2.9 22.2 + - - +
235A GLY* 1.3 76.3 - - - +
237A VAL* 1.3 60.5 + - + +
239A ILE* 3.3 7.9 + - - -
240A THR* 2.9 24.0 + - - -
272A TYR* 4.0 12.6 - - + +
298A LYS* 6.1 0.9 - - - +
304A ARG* 2.9 23.2 + - - +
2D GCD 5.9 0.7 - - - +
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 3.9 16.2 - - + +
177A THR* 4.4 2.3 + - - +
178A ASP* 3.2 36.5 - - - +
233A SER 3.2 10.2 + - - +
234A TYR* 2.9 8.4 + - + +
236A ALA* 1.3 74.3 - - + +
238A PHE* 1.3 66.6 + - - +
240A THR* 3.2 8.7 + - + -
241A GLY* 3.0 21.7 + - - -
1D ASG 4.2 12.6 - - + +
2D GCD 3.3 29.2 - - + +
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Residues in contact with PHE 238 (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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173A GLY 5.6 0.4 - - - -
174A ALA* 4.3 3.3 - - + +
177A THR* 4.4 16.4 + - + -
206A PRO* 3.9 40.8 - - + -
207A VAL* 4.1 16.8 - - + -
216A LEU* 5.0 10.3 - - + -
222A TYR* 3.8 37.2 - + + +
234A TYR 2.8 12.0 + - - +
235A GLY 3.3 12.8 - - - +
237A VAL* 1.3 76.1 - - - +
239A ILE* 1.3 64.3 + - + +
241A GLY* 3.5 0.3 + - - -
242A VAL* 3.1 49.2 + - + +
264A PHE* 5.1 10.1 - + - -
267A TYR* 4.2 26.9 - + + -
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Residues in contact with ILE 239 (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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235A GLY 3.0 16.9 + - - +
236A ALA* 3.5 9.0 - - - +
237A VAL 3.2 0.2 - - - -
238A PHE* 1.3 78.8 - - + +
240A THR* 1.3 63.4 + - - +
243A LEU* 2.9 30.5 + - + +
264A PHE* 3.8 24.4 - - + -
267A TYR* 3.5 35.2 - - + -
268A TYR* 3.8 29.2 - - + -
272A TYR* 3.8 33.0 - - + -
304A ARG* 3.9 19.3 - - - +
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Residues in contact with THR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP* 6.2 0.9 - - - +
236A ALA 2.9 10.2 + - - -
237A VAL* 3.2 12.4 + - + -
239A ILE* 1.3 76.3 - - - +
241A GLY* 1.3 63.2 + - - +
243A LEU* 3.8 1.9 - - - +
244A LYS* 3.1 50.9 + - + +
304A ARG* 2.7 38.4 + - - +
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Residues in contact with GLY 241 (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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177A THR* 5.0 8.5 - - - -
178A ASP* 5.6 4.5 + - - -
181A LEU* 5.3 5.6 - - - -
203A LEU* 3.6 16.3 - - - +
237A VAL 3.0 14.3 + - - -
238A PHE 4.0 0.7 - - - -
240A THR* 1.3 78.1 - - - +
242A VAL* 1.3 61.9 + - - +
244A LYS* 3.3 12.1 - - - +
245A LEU* 3.1 24.3 + - - +
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 4.8 1.8 - - + -
203A LEU* 3.7 22.2 - - + +
204A PHE* 3.9 12.0 - - + -
207A VAL* 3.8 21.8 - - + -
238A PHE* 3.1 43.6 + - + +
241A GLY* 1.3 73.9 - - - +
243A LEU* 1.3 57.7 + - - +
246A ALA* 2.9 29.6 + - + +
256A LEU* 4.4 9.6 - - + -
264A PHE* 3.5 33.2 - - + -
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 2.9 20.2 + - + +
240A THR 3.8 3.1 - - - +
242A VAL* 1.3 78.3 - - - +
244A LYS* 1.3 62.8 + - - +
246A ALA* 3.5 2.9 + - + -
247A ASN* 3.1 22.0 + - - +
264A PHE* 3.8 27.1 - - + -
268A TYR* 4.4 10.8 - - + -
304A ARG* 3.3 49.6 - - + +
307A VAL* 4.0 14.1 - - + -
308A ALA* 4.0 22.9 - - + +
311A ILE* 3.7 9.8 - - + +
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Residues in contact with LYS 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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38A ASP* 4.6 7.5 + - - +
39A LEU* 6.2 1.9 - - - +
139A GLU* 5.2 4.8 + - - -
181A LEU* 4.2 20.1 - - + +
185A TYR* 4.4 13.4 + - - -
240A THR* 3.1 40.1 + - + +
241A GLY* 3.3 10.8 - - - +
243A LEU* 1.3 79.3 - - - +
245A LEU* 1.3 66.0 + - - +
247A ASN* 3.2 9.0 + - - +
248A TYR* 2.9 57.5 + - + +
307A VAL* 5.6 1.6 - - - -
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Residues in contact with LEU 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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181A LEU* 5.4 1.1 - - + -
184A PHE* 3.6 46.2 - - + -
199A ALA 5.4 0.4 - - - -
200A VAL* 4.1 15.5 - - + -
203A LEU* 3.6 38.1 - - + -
204A PHE* 3.6 31.2 - - + -
241A GLY 3.1 17.8 + - - +
244A LYS* 1.3 75.5 - - + +
246A ALA* 1.3 67.4 + - - +
248A TYR* 2.8 15.7 + - - +
249A VAL* 2.8 26.4 + - + +
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Residues in contact with ALA 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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204A PHE* 3.8 10.4 - - + -
242A VAL* 2.9 20.7 + - + +
243A LEU* 3.8 6.3 - - + +
245A LEU* 1.3 75.5 - - - +
247A ASN* 1.3 57.5 + - - +
249A VAL* 3.9 3.4 - - - +
250A ARG* 3.0 31.4 + - - +
256A LEU* 4.0 29.7 + - + -
261A LEU* 5.1 1.3 - - + -
264A PHE* 6.3 1.6 - - + -
311A ILE* 3.8 19.6 - - + +
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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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34A ARG* 3.8 5.9 + - - +
38A ASP* 5.0 8.9 + - - +
243A LEU 3.1 10.1 + - - +
244A LYS* 3.4 9.8 - - - +
245A LEU 3.0 0.4 - - - -
246A ALA* 1.3 79.3 - - - +
248A TYR* 1.3 76.2 + - - +
250A ARG* 3.2 37.1 + - - +
307A VAL* 3.7 25.3 - - + +
310A MET* 5.2 9.4 - - - +
311A ILE* 3.2 23.9 - - + +
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Residues in contact with TYR 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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31A ILE* 3.7 17.3 - - + +
34A ARG* 2.9 33.8 + - + +
35A VAL* 3.8 38.0 + - + +
38A ASP* 2.5 45.3 + - + +
39A LEU* 5.2 4.7 - - - +
181A LEU* 5.0 1.6 - - + -
184A PHE* 3.6 37.5 - + + -
185A TYR* 4.7 8.8 + + - -
244A LYS* 2.9 50.0 + - + -
245A LEU* 2.8 10.5 + - + +
247A ASN* 1.3 88.1 - - - +
249A VAL* 1.3 58.5 + - - +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 4.0 15.7 - - + -
184A PHE* 4.4 7.0 - - + -
200A VAL* 4.5 4.9 - - + -
204A PHE* 4.1 10.3 - - + -
245A LEU* 2.8 45.2 + - + +
246A ALA* 4.0 7.9 - - - +
248A TYR* 1.3 73.7 - - - +
250A ARG* 1.3 66.8 + - - +
251A ASP 3.4 0.2 + - - -
252A THR* 2.5 34.8 + - - +
254A TYR* 3.4 35.9 - - + +
255A ALA* 3.5 9.9 - - - -
256A LEU 4.4 0.2 - - - +
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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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34A ARG* 2.7 50.0 + - - +
246A ALA 3.0 14.5 + - - +
247A ASN* 3.2 38.4 + - - +
248A TYR 3.4 0.4 - - - -
249A VAL* 1.3 77.6 - - - +
251A ASP* 1.3 88.1 + - - +
252A THR* 3.4 1.0 - - - +
255A ALA* 4.4 5.8 - - - -
256A LEU 5.8 0.2 - - - +
310A MET* 5.4 15.6 - - - +
311A ILE* 4.5 15.0 - - + +
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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
------------------------------------------------------------
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