Contacts of the helix formed by residues 239 - 256 (chain A) in PDB entry 1UMD
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 ASP 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG 3.7 0.9 - - - -
18A LEU 2.8 25.1 + - - -
19A ILE* 2.8 31.0 + - - +
75A ALA* 4.0 1.1 - - - -
236A ASP* 3.0 22.8 + - - +
238A MET* 1.3 78.4 - - - +
240A VAL* 1.3 57.4 + - - +
241A LEU* 3.0 6.9 + - - +
242A ALA* 2.8 26.5 + - + -
243A SER* 2.9 30.9 + - - -
299A ARG* 3.3 16.1 + - - +
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Residues in contact with VAL 240 (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 ILE* 4.3 2.0 - - + +
41A LEU* 4.4 20.4 - - + -
45A MET* 3.8 27.4 - - + -
75A ALA* 3.6 30.7 - - + +
78A VAL* 4.7 0.9 - - + -
79A ALA* 3.7 9.9 - - + +
238A MET 3.8 1.2 + - - -
239A ASP* 1.3 72.5 + - - +
241A LEU* 1.3 64.2 + - + +
243A SER* 4.4 0.2 - - - -
244A TYR* 3.0 27.5 + - - +
296A PRO 5.8 0.6 + - - +
300A PHE* 3.6 47.1 - - + +
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Residues in contact with LEU 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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18A LEU* 3.7 13.2 - - + -
19A ILE* 3.8 16.2 - - + -
25A TRP* 3.8 14.4 - - + -
31A LEU* 4.6 2.9 - - + -
33A LEU* 4.0 9.6 - - + -
38A LEU* 3.9 22.2 - - + -
41A LEU* 4.0 15.9 - - + -
239A ASP* 3.0 7.8 + - - +
240A VAL* 1.3 74.9 - - + +
242A ALA* 1.3 64.8 + - - +
244A TYR* 3.7 2.0 - - + +
245A TYR* 2.9 36.2 + - + +
300A PHE* 3.9 16.6 - - + -
303A PHE* 3.6 37.5 - - + -
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Residues in contact with ALA 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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16A ILE* 3.6 26.9 - - + +
17A ARG* 4.0 0.7 - - - -
18A LEU* 3.7 20.6 - - + +
235A VAL* 3.8 8.1 - - + -
239A ASP* 2.8 31.1 + - + +
241A LEU* 1.3 76.2 - - - +
243A SER* 1.3 63.6 + - - +
246A VAL* 3.0 31.9 + - - +
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Residues in contact with SER 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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75A ALA 4.1 6.2 + - - -
76A ALA* 4.3 5.3 - - - -
79A ALA* 3.6 18.4 - - - -
235A VAL* 4.0 1.1 - - - +
236A ASP 3.5 11.6 + - - -
237A GLY* 3.6 16.5 + - - -
239A ASP 2.9 18.3 + - - -
240A VAL 3.9 0.4 - - - -
242A ALA* 1.3 77.3 - - - +
244A TYR* 1.3 62.1 + - - +
246A VAL* 4.2 0.8 - - - +
247A VAL* 3.0 30.7 + - - +
265A LEU* 3.7 22.5 - - - +
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Residues in contact with TYR 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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33A LEU* 3.7 26.3 - - + +
37A LYS* 3.3 27.4 - - - -
41A LEU* 4.9 10.3 - - + -
79A ALA* 3.4 30.0 - - + +
82A HIS* 3.3 30.5 + - + -
83A ALA* 3.9 7.6 - - - +
240A VAL 3.0 19.5 + - - +
241A LEU* 3.7 3.6 - - - +
242A ALA 3.3 0.2 - - - -
243A SER* 1.3 76.6 - - - +
245A TYR* 1.3 89.7 - + - +
247A VAL* 3.9 1.3 - - - +
248A LYS* 2.8 59.4 + - + +
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Residues in contact with TYR 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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8A PHE* 3.6 23.6 - + + -
18A LEU* 3.7 12.8 - - + -
25A TRP* 3.8 17.7 - + - -
29A PHE* 3.8 23.1 - + - -
31A LEU* 3.5 8.8 - - + +
32A ASP* 2.5 48.0 + - - -
33A LEU* 3.4 18.5 + - + +
241A LEU* 2.9 31.4 + - + +
244A TYR* 1.3 95.9 - + - +
246A VAL* 1.3 58.4 + - - +
248A LYS* 3.7 6.9 - - + +
249A GLU* 3.0 29.1 + - - +
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Residues in contact with VAL 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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8A PHE* 3.9 35.0 - - + -
16A ILE* 4.1 11.7 - - + -
233A TYR* 3.8 31.1 - - + -
235A VAL* 3.7 31.2 - - + -
242A ALA 3.0 19.8 + - - +
243A SER* 4.3 1.3 - - - +
245A TYR* 1.3 75.3 - - - +
247A VAL* 1.3 63.3 + - - +
249A GLU* 3.3 4.6 + - - +
250A ALA* 3.1 19.8 + - - +
263A VAL* 3.8 9.6 - - + -
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Residues in contact with VAL 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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80A ILE* 4.4 20.0 - - + -
83A ALA* 3.7 18.4 - - + -
84A ILE* 5.7 0.2 - - + -
170A VAL* 5.3 1.6 - - + -
198A VAL* 4.7 2.5 - - + -
200A ILE* 3.8 32.8 - - + -
243A SER 3.0 20.9 + - - +
244A TYR* 3.9 2.0 - - - +
246A VAL* 1.3 77.2 - - - +
248A LYS* 1.3 58.2 + - - +
250A ALA* 3.0 8.0 + - - +
251A VAL* 2.8 35.7 + - + +
263A VAL* 4.2 20.0 - - + -
265A LEU* 4.5 8.3 - - + -
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Residues in contact with LYS 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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37A LYS* 5.7 1.0 - - - +
82A HIS 5.0 3.6 + - - -
83A ALA* 3.7 28.3 + - + +
85A ARG* 6.1 1.4 - - - +
244A TYR* 2.8 52.0 + - + +
245A TYR* 3.7 10.8 - - + +
247A VAL* 1.3 77.1 - - - +
249A GLU* 1.3 55.7 + - - +
251A VAL* 3.2 5.2 + - + +
252A GLU* 2.9 62.1 + - + +
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Residues in contact with GLU 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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6A HIS* 3.6 11.9 + - - +
7A ARG* 3.3 16.5 - - - +
8A PHE* 2.9 44.6 + - + -
233A TYR* 3.4 12.9 + - + -
245A TYR 3.0 18.9 + - - +
246A VAL* 3.6 5.6 - - - +
248A LYS* 1.3 76.2 - - - +
250A ALA* 1.3 58.5 + - - +
252A GLU* 3.3 15.7 + - - +
253A ARG* 2.9 54.8 + - - +
256A ARG* 5.3 3.3 + - - +
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Residues in contact with ALA 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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198A VAL* 3.7 20.6 - - + +
233A TYR* 5.1 1.3 - - + -
246A VAL 3.1 11.8 + - - +
247A VAL 3.0 9.7 + - - +
249A GLU* 1.3 76.4 - - - +
251A VAL* 1.3 57.7 + - - +
253A ARG* 3.3 16.4 + - - +
254A ALA* 3.0 28.1 + - - +
259A GLY 4.9 0.3 - - - +
260A PRO 6.0 0.2 - - - -
261A SER* 3.8 26.9 + - - -
263A VAL* 4.1 8.7 - - + -
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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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83A ALA 3.9 21.5 - - - +
84A ILE* 4.0 17.5 - - + -
168A VAL* 3.7 10.2 - - + +
170A VAL* 4.3 4.0 - - + -
198A VAL* 3.9 17.5 - - + -
247A VAL* 2.8 27.8 + - + +
248A LYS* 3.4 7.9 - - + +
250A ALA* 1.3 77.6 - - - +
252A GLU* 1.3 58.3 + - + +
254A ALA* 3.3 4.0 + - - +
255A ARG* 2.8 58.6 + - - +
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Residues in contact with GLU 252 (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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248A LYS* 2.9 51.2 + - + +
249A GLU* 3.7 14.8 - - - +
251A VAL* 1.3 75.7 - - + +
253A ARG* 1.3 66.1 + - - +
255A ARG* 3.3 10.2 + - - +
256A ARG* 3.0 44.6 + - - +
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Residues in contact with ARG 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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7A ARG* 3.2 33.1 - - - +
231A PRO* 4.1 14.1 - - - +
233A TYR* 2.7 32.7 + - - -
249A GLU* 2.9 35.9 + - - +
250A ALA* 3.4 19.1 - - - +
251A VAL 3.2 0.2 - - - -
252A GLU* 1.3 76.9 - - - +
254A ALA* 1.3 61.0 + - - +
256A ARG* 3.4 20.9 + - - +
258A GLU* 3.0 53.8 + - + +
259A GLY 3.8 10.1 - - - +
260A PRO 4.6 1.1 - - - -
261A SER* 3.0 28.4 + - - -
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Residues in contact with ALA 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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168A VAL* 4.0 10.1 - - + -
196A PRO* 3.5 46.0 - - + +
197A ALA 4.1 2.2 - - - +
198A VAL* 4.3 4.7 - - + -
250A ALA 3.0 13.4 + - - +
251A VAL 3.6 8.3 - - - +
252A GLU 3.3 0.2 - - - -
253A ARG* 1.3 76.0 - - - +
255A ARG* 1.3 63.4 + - - +
257A GLY* 3.0 15.2 + - - -
259A GLY 3.7 17.4 + - - +
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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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83A ALA 4.9 0.8 + - - -
84A ILE* 4.7 1.8 - - - +
85A ARG* 4.4 18.7 - - - +
88A PHE* 3.6 9.7 - - - -
89A ASP* 2.8 41.4 + - - -
166A GLY* 2.9 37.2 + - - +
167A GLN 5.3 0.7 - - - -
168A VAL* 3.7 13.7 - - + +
196A PRO* 5.0 1.3 - - - -
251A VAL* 2.8 37.8 + - - +
252A GLU* 3.3 10.0 + - - +
254A ALA* 1.3 77.8 - - - +
256A ARG* 1.3 58.8 + - - +
257A GLY 3.2 0.7 + - - -
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Residues in contact with ARG 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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7A ARG* 3.2 17.6 - - - +
249A GLU* 5.3 3.0 + - - +
252A GLU* 3.0 37.2 + - - +
253A ARG* 3.4 15.8 - - - +
254A ALA 3.2 0.6 - - - -
255A ARG* 1.3 76.8 - - - +
257A GLY* 1.3 57.6 + - - +
258A GLU* 2.7 60.8 + - + +
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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