Contacts of the helix formed by residues 284 - 303 (chain A) in PDB entry 1PEA
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 ALA 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A SER* 5.0 2.3 - - - -
236A GLU* 4.1 5.3 + - - +
254A ALA* 3.9 16.6 - - + -
255A PRO* 4.8 2.7 - - + +
256A TYR* 3.1 45.4 + - + +
257A PHE* 5.6 0.4 - - + -
283A THR* 1.3 76.2 - - - +
285A TRP* 1.3 75.2 + - + +
287A GLU* 3.2 5.4 - - - +
288A ALA* 3.0 26.0 + - - +
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Residues in contact with TRP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.5 26.7 - - + -
27A GLN* 3.7 26.1 - - + +
83A TYR* 4.3 8.5 - + - -
105A PRO 3.7 15.3 - - - +
107A PRO* 3.6 40.5 - - + +
121A GLY* 4.3 4.3 - - - -
122A PRO* 3.6 22.9 - - + -
232A LEU 3.7 12.3 - - - -
233A THR* 3.6 22.1 + - - +
234A THR 5.5 0.2 + - - -
235A SER* 4.5 7.9 - - - -
253A VAL 4.9 0.2 - - - -
254A ALA* 4.2 15.0 - - + -
255A PRO* 3.5 30.7 - - + -
283A THR* 3.1 6.3 + - - +
284A ALA* 1.3 84.9 - - + +
286A ALA* 1.3 63.9 + - - +
287A GLU 3.2 0.9 - - - -
288A ALA* 3.5 7.9 + - + +
289A ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 2.9 42.1 + - - +
27A GLN* 3.9 5.4 - - - +
30A GLY* 3.6 7.5 - - - -
268A PHE* 4.5 5.8 - - + -
276A PHE* 4.3 17.0 - - + -
283A THR* 3.1 16.6 + - - +
285A TRP* 1.3 75.4 - - - +
287A GLU* 1.3 57.0 + - - +
289A ALA 3.3 1.2 + - - -
290A TYR* 2.9 29.9 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO* 5.7 0.9 - - - +
256A TYR* 3.7 28.9 - - + +
268A PHE* 3.9 13.1 - - + -
283A THR 3.2 10.5 + - - +
284A ALA 3.2 11.5 - - - +
286A ALA* 1.3 79.1 - - - +
288A ALA* 1.3 58.6 + - - +
290A TYR* 3.3 4.2 - - - +
291A TRP* 3.0 26.3 + - - -
322A ALA* 3.3 9.7 - - - +
323A PRO* 3.1 41.5 - - + +
324A GLN* 3.2 40.0 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 3.7 21.5 - - + +
120A GLY 3.8 21.1 - - - +
255A PRO* 6.2 1.8 - - + -
284A ALA 3.0 12.6 + - - +
285A TRP* 3.7 14.6 - - + +
286A ALA 3.4 0.2 - - - -
287A GLU* 1.3 73.6 + - - +
289A ALA* 1.3 66.5 + - - +
290A TYR 3.2 0.2 - - - -
291A TRP* 3.5 14.9 + - - +
292A GLN* 3.0 29.3 + - - +
324A GLN* 5.8 0.7 - - - +
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Residues in contact with ALA 289 (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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14A PHE* 4.5 0.2 - - + -
27A GLN* 3.3 28.0 - - - +
31A ALA* 4.0 5.6 - - + +
80A VAL* 4.3 12.0 - - + +
105A PRO* 3.5 23.5 - - + +
285A TRP 3.0 16.4 + - - +
286A ALA 3.3 2.4 + - - +
288A ALA* 1.3 76.2 - - - +
290A TYR* 1.3 55.0 + - - +
292A GLN* 4.4 1.7 - - - +
293A THR* 2.5 36.7 + - - -
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Residues in contact with TYR 290 (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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30A GLY 3.4 23.1 + - - +
33A LEU* 3.8 24.9 - - + -
34A ALA* 3.4 23.7 - - + +
37A GLN* 2.9 37.9 + - - -
268A PHE* 4.1 18.1 - + + -
286A ALA 2.9 15.0 + - - +
287A GLU 3.3 9.0 - - - +
289A ALA* 1.3 74.4 - - - +
291A TRP* 1.4 68.1 + - - +
293A THR 3.2 2.1 + - - -
294A LEU* 3.1 40.1 + - + +
323A PRO* 3.9 34.3 - - + -
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Residues in contact with TRP 291 (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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120A GLY* 4.0 18.5 + - - -
287A GLU* 3.0 28.6 + - - +
288A ALA* 3.5 31.3 - - - +
290A TYR* 1.4 78.4 - - + +
292A GLN* 1.3 80.6 + - + +
294A LEU* 3.2 9.0 + - - +
295A LEU* 3.1 49.6 + - + +
320A ILE* 4.2 11.9 - - + +
322A ALA* 3.7 24.9 - - + -
324A GLN* 3.8 16.1 - - - +
327A VAL* 3.8 22.0 - - + -
328A ARG 4.9 1.8 - - - -
329A VAL* 3.9 10.5 - - + -
336A SER* 3.3 35.2 - - - -
338A LEU* 4.1 3.8 - - + +
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Residues in contact with GLN 292 (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 VAL* 5.8 0.9 - - + -
103A CYS* 3.5 30.0 - - + +
104A TYR 3.8 10.7 - - - +
105A PRO* 3.9 4.0 - - - +
118A VAL* 2.7 53.2 + - + +
120A GLY* 3.4 26.4 + - - +
288A ALA 3.0 18.8 + - - +
289A ALA* 4.4 3.4 - - - +
291A TRP* 1.3 100.5 - - + +
293A THR* 1.3 57.8 + - - +
295A LEU* 3.8 4.6 - - + +
296A LEU* 3.1 25.8 + - - +
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Residues in contact with THR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.5 14.7 - - + +
12A LEU* 6.2 0.4 - - + -
31A ALA* 3.9 12.6 - - + +
34A ALA* 3.4 16.2 - - + -
35A VAL* 3.7 29.2 - - + -
38A LEU* 3.5 7.8 - - + +
80A VAL* 3.7 22.8 - - + +
289A ALA 2.5 25.1 + - - -
291A TRP 3.2 0.4 - - - -
292A GLN* 1.3 74.8 - - - +
294A LEU* 1.3 64.4 + - - +
296A LEU* 3.2 6.8 + - + +
297A GLY 3.1 15.4 + - - -
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Residues in contact with LEU 294 (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 ALA* 4.0 8.7 - - + +
37A GLN* 4.2 21.5 - - + +
38A LEU* 4.0 26.5 - - + -
290A TYR* 3.1 39.3 + - + +
291A TRP* 3.4 8.1 - - + +
293A THR* 1.3 74.2 - - - +
295A LEU* 1.3 51.5 - - - +
297A GLY* 2.6 25.3 + - - -
298A ARG* 2.6 34.6 + - - +
320A ILE* 3.7 30.7 - - + -
321A ASP 5.7 1.8 - - - +
322A ALA* 5.9 0.2 - - - -
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Residues in contact with LEU 295 (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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118A VAL* 5.7 0.2 - - + -
291A TRP* 3.1 37.1 + - + +
292A GLN* 3.8 7.4 - - + +
294A LEU* 1.3 79.0 - - - +
296A LEU* 1.3 64.0 + - - +
298A ARG* 4.2 2.0 - - - -
299A ALA* 2.8 28.1 + - - +
315A LEU* 3.7 31.4 - - + +
318A ILE* 3.4 47.8 - - + +
320A ILE* 3.8 16.5 - - + +
328A ARG* 5.8 0.9 - - - -
329A VAL* 3.6 22.4 - - + +
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Residues in contact with LEU 296 (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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10A ILE* 4.8 12.6 - - + -
78A PHE* 3.9 36.1 - - + -
79A LEU 4.9 3.8 - - - +
80A VAL* 4.5 15.9 - - + -
101A LEU* 4.1 24.7 - - + +
103A CYS* 4.1 28.9 - - - -
292A GLN 3.1 12.2 + - - +
293A THR* 3.5 10.1 - - + +
294A LEU 3.2 0.4 - - - -
295A LEU* 1.3 75.3 - - - +
297A GLY* 1.3 63.9 + - - +
299A ALA* 4.0 3.4 - - - +
300A ALA* 3.3 21.1 + - - +
306A TRP* 4.6 8.8 - - + -
311A VAL* 4.2 5.1 - - + +
315A LEU* 4.1 14.8 - - + -
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Residues in contact with GLY 297 (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 LEU* 4.1 16.6 - - - -
44A VAL* 4.4 10.6 - - - +
49A ILE* 5.0 3.6 - - - -
293A THR 3.1 7.8 + - - -
294A LEU 2.6 15.2 + - - -
296A LEU* 1.3 69.2 - - - +
298A ARG* 1.3 66.9 + - - -
300A ALA* 2.8 16.5 + - - +
301A GLN* 3.0 18.4 + - - +
306A TRP* 5.3 2.7 - - - -
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Residues in contact with ARG 298 (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 LEU* 3.4 17.1 - - - +
41A GLU* 2.7 40.2 + - - -
294A LEU* 2.6 41.4 + - - +
295A LEU* 3.9 4.9 - - - +
297A GLY* 1.3 71.7 - - - +
299A ALA* 1.3 62.1 + - - +
301A GLN* 3.0 28.5 + - - +
302A ALA* 3.0 25.1 + - - +
318A ILE* 3.7 22.2 - - + -
320A ILE* 4.4 11.6 - - + +
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Residues in contact with ALA 299 (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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295A LEU 2.8 22.2 + - - +
296A LEU 4.0 0.2 - - - +
298A ARG* 1.3 73.1 - - - +
300A ALA* 1.3 56.1 - - - +
302A ALA* 3.7 2.1 - - - +
303A ALA* 2.9 30.2 + - - +
311A VAL* 3.7 33.4 - - + +
314A HIS* 3.7 9.6 - - + +
315A LEU* 4.1 10.1 - - + +
318A ILE* 3.2 20.3 - - + +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.3 5.1 - - + +
296A LEU 3.3 11.4 + - - +
297A GLY 2.8 11.1 + - - +
299A ALA* 1.3 78.8 - - - +
301A GLN* 1.3 54.2 + - - +
303A ALA* 4.2 0.9 - - - +
304A GLY* 2.6 27.4 + - - -
305A ASN 3.0 24.0 + - - +
306A TRP* 3.4 32.8 - - + +
311A VAL* 4.1 11.4 - - + +
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Residues in contact with GLN 301 (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 LEU* 4.5 4.9 - - - +
41A GLU* 4.1 7.3 + - - -
43A GLY 3.9 16.2 + - - -
44A VAL* 4.0 24.2 - - + +
45A GLY 5.4 2.2 - - - +
297A GLY 3.0 11.9 + - - +
298A ARG* 3.4 47.9 + - - +
300A ALA* 1.3 75.3 - - - +
302A ALA* 1.3 57.0 + - - +
304A GLY* 2.8 24.8 + - - -
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Residues in contact with ALA 302 (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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298A ARG 3.0 12.3 + - - +
299A ALA* 3.7 6.5 - - - +
301A GLN* 1.3 81.6 - - - +
303A ALA* 1.3 59.6 + - - +
304A GLY* 3.3 0.5 + - - -
314A HIS* 3.8 26.0 + - + -
318A ILE* 5.0 5.4 - - + -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA 2.9 20.0 + - - +
300A ALA* 4.0 4.9 - - - +
302A ALA* 1.3 76.2 - - - +
304A GLY* 1.3 62.7 + - - +
305A ASN* 3.9 7.9 - - - +
310A ASP* 3.4 42.5 - - + +
311A VAL* 4.1 2.9 - - - +
314A HIS* 3.5 14.5 + - + +
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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
------------------------------------------------------------
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