Contacts of the helix formed by residues 282 - 301 (chain A) in PDB entry 5XOU
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 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LEU* 1.3 89.7 - - + +
283A TRP* 1.3 68.0 + - + +
284A GLU* 3.2 17.9 - - + +
285A GLU* 3.1 31.1 + - + +
286A ARG 3.1 16.5 + - - -
609A ASP 4.9 12.1 - - - +
612A GLY* 5.0 0.4 - - - -
613A THR* 3.7 0.9 + - - -
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Residues in contact with TRP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU 3.5 1.6 + - - -
282A PRO* 1.3 72.3 - - + +
284A GLU* 1.3 84.3 + - + +
286A ARG* 3.4 1.0 + - - +
287A ARG* 2.9 70.9 + - - +
582A TYR* 3.5 19.2 - + + -
583A PRO* 3.6 20.4 - - + -
586A GLY 3.5 18.6 - - - -
587A ARG* 4.1 4.8 - - - +
588A LEU* 3.6 39.2 - - + +
607A HIS* 4.1 20.0 - + + -
609A ASP* 4.2 18.6 + - - -
612A GLY 4.9 0.8 - - - -
613A THR* 3.2 34.4 - - + +
614A PRO* 4.4 1.8 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO* 4.2 13.2 - - + +
283A TRP* 1.3 117.4 + - + +
285A GLU* 1.3 63.3 + - - +
287A ARG* 3.2 13.0 + - - +
288A ARG* 3.0 26.1 + - - +
609A ASP* 5.0 5.4 - - - +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.6 11.9 - - + -
282A PRO* 3.1 38.9 + - + +
284A GLU* 1.3 80.0 - - - +
286A ARG* 1.3 64.6 + - - +
288A ARG* 2.9 35.6 + - - +
289A ARG* 3.0 43.2 + - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 3.1 20.2 + - - -
169A PRO* 2.9 41.2 + - + +
281A LEU* 3.7 35.0 - - + +
282A PRO 3.1 2.7 + - - +
283A TRP 3.6 4.3 - - - +
285A GLU* 1.3 79.1 - - - +
287A ARG* 1.3 53.0 + - - +
289A ARG* 3.8 0.9 - - - +
290A THR* 2.6 37.3 + - - -
580A ARG* 3.4 19.9 - - - +
582A TYR* 3.1 19.5 - - - +
613A THR* 3.1 30.2 + - - +
7C A 2.8 40.5 + - - -
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.9 11.9 - - - -
283A TRP* 2.9 46.4 + - - +
284A GLU* 3.4 15.1 + - - +
285A GLU 3.2 0.2 - - - -
286A ARG* 1.3 77.4 - - - +
288A ARG* 1.3 63.3 + - - +
290A THR* 3.2 6.9 + - - +
291A ARG* 3.1 38.1 + - - +
582A TYR* 3.9 37.6 - - + -
583A PRO 2.8 26.3 + - - -
584A VAL* 4.2 9.1 + - - +
585A GLN* 5.6 0.8 - - - +
586A GLY 5.0 2.2 + - - +
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Residues in contact with ARG 288 (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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284A GLU 3.0 10.3 + - - +
285A GLU* 2.9 53.2 + - - +
287A ARG* 1.3 79.3 - - - +
289A ARG* 1.3 65.1 + - + +
291A ARG* 3.0 12.1 + - + +
292A GLU* 2.9 42.5 + - + +
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Residues in contact with ARG 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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138A GLU 5.2 5.7 + - - -
149A GLY* 4.6 18.4 - - - -
150A GLY 4.9 4.8 + - - +
169A PRO* 4.0 23.3 - - + +
170A ALA 5.4 2.6 + - - -
281A LEU* 3.5 34.8 - - - +
285A GLU* 3.0 26.7 + - + +
286A ARG* 3.9 2.9 - - - +
288A ARG* 1.3 82.2 - - + +
290A THR* 1.3 61.9 + - - +
292A GLU* 3.7 18.1 - - - +
293A ILE* 2.9 37.7 + - + +
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Residues in contact with THR 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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12A ASN* 4.3 11.3 - - + +
14A PHE* 3.7 23.8 - - + -
167A VAL* 3.5 31.9 + - + +
168A ASP* 4.7 0.3 + - - -
169A PRO* 3.4 18.6 - - - +
286A ARG 2.6 23.7 + - - -
287A ARG* 3.2 13.5 - - - +
288A ARG 3.1 0.2 - - - -
289A ARG* 1.3 76.5 - - - +
291A ARG* 1.3 57.6 + - - +
294A ALA* 2.9 27.2 + - - +
582A TYR* 4.0 10.9 + - + -
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Residues in contact with ARG 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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10A PHE* 3.9 37.6 - - - +
14A PHE* 4.2 17.9 - - + -
287A ARG* 3.1 27.3 + - - +
288A ARG* 3.0 13.6 + - + +
290A THR* 1.3 73.3 - - - +
292A GLU* 1.3 62.6 + - + +
294A ALA* 3.3 2.3 + - - +
295A SER* 2.8 34.9 + - - -
308A ALA* 3.9 25.2 - - - +
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Residues in contact with GLU 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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288A ARG* 2.9 33.0 + - + +
289A ARG* 3.7 22.0 - - - +
291A ARG* 1.3 82.0 - - + +
293A ILE* 1.3 61.6 + - + +
295A SER* 3.2 4.8 + - - -
296A TRP* 3.0 30.5 + - - +
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Residues in contact with ILE 293 (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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134A VAL* 5.4 1.3 - - + -
136A ARG* 6.1 4.9 - - + -
150A GLY* 3.5 30.5 - - - +
151A ALA* 3.6 25.8 - - + -
153A LEU* 4.4 0.9 - - + -
167A VAL* 3.6 12.3 - - + -
169A PRO* 4.7 6.7 - - + -
289A ARG* 2.9 31.4 + - + +
292A GLU* 1.3 77.9 - - + +
294A ALA* 1.3 63.6 + - - +
296A TRP* 3.8 8.5 - - + +
297A ILE* 2.9 43.8 + - + +
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Residues in contact with ALA 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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14A PHE* 3.6 42.2 - - + -
165A LEU* 4.2 6.7 - - + +
167A VAL* 4.1 12.8 - - + +
290A THR 2.9 20.1 + - - +
291A ARG 3.3 5.8 + - - +
293A ILE* 1.3 77.3 - - - +
295A SER* 1.3 56.6 + - - +
297A ILE* 3.9 1.2 - - - +
298A GLY* 2.9 23.4 + - - -
306A PRO* 3.5 12.1 - - + +
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 2.8 18.4 + - - +
292A GLU* 3.5 5.2 + - - -
294A ALA* 1.3 74.1 - - - +
296A TRP* 1.3 69.4 + - - +
298A GLY 3.1 9.4 + - - -
299A ARG* 3.1 16.1 + - - +
305A THR* 5.9 0.2 - - - -
306A PRO* 3.4 21.3 - - - +
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Residues in contact with TRP 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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124A LEU* 5.7 4.3 - - + -
127A VAL* 4.6 20.4 - - + -
134A VAL* 5.3 8.1 - - + -
136A ARG* 4.7 20.9 - - + -
292A GLU 3.0 18.4 + - - +
293A ILE* 3.8 8.1 - - + +
295A SER* 1.3 77.4 - - - +
297A ILE* 1.3 88.3 + - + +
299A ARG* 4.9 0.9 - - - +
300A ARG* 3.3 56.1 + - - +
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Residues in contact with ILE 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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117A LEU* 5.1 0.9 - - + -
121A LEU* 4.6 8.7 - - + -
124A LEU* 6.4 1.1 - - + -
134A VAL* 4.1 8.7 - - + -
153A LEU* 3.8 31.2 - - + -
165A LEU* 4.0 25.6 - - + -
167A VAL* 6.0 0.2 - - + -
293A ILE* 2.9 37.9 + - + +
294A ALA 3.9 2.0 - - - +
296A TRP* 1.3 104.4 - - + +
298A GLY* 1.3 59.0 + - - +
300A ARG* 3.4 4.4 + - + -
301A LEU* 2.9 47.1 + - + +
303A LEU* 6.2 1.8 - - + -
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Residues in contact with GLY 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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16A LEU* 4.5 14.6 - - - -
165A LEU* 5.0 1.6 - - - -
294A ALA 2.9 20.2 + - - -
295A SER 3.1 2.6 + - - -
297A ILE* 1.3 78.2 - - - +
299A ARG* 1.3 60.7 + - - +
301A LEU* 5.0 0.2 - - - -
302A GLY 3.4 1.4 + - - -
303A LEU* 3.0 30.5 + - - +
304A GLY 3.2 16.5 - - - +
306A PRO* 4.6 1.6 - - - -
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Residues in contact with ARG 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 SER 3.1 14.0 + - - +
296A TRP 4.9 0.7 - - - +
298A GLY* 1.3 73.9 - - - +
300A ARG* 1.3 64.5 + - - +
302A GLY* 2.8 22.3 + - - -
304A GLY* 3.7 11.0 + - - +
305A THR* 6.2 0.2 - - - -
306A PRO* 5.2 0.4 - - - +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.0 38.4 - - + +
125A GLU 4.2 15.8 + - - -
296A TRP* 3.3 59.1 + - - +
297A ILE* 3.4 5.1 + - + +
298A GLY 3.3 0.2 - - - -
299A ARG* 1.3 85.0 - - - +
301A LEU* 1.3 63.2 + - + +
302A GLY 3.1 0.7 + - - -
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Residues in contact with LEU 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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116A LEU* 5.8 0.4 - - + -
117A LEU* 3.6 31.9 - - + -
120A ARG* 2.9 64.9 + - + +
121A LEU* 3.7 17.7 - - + -
124A LEU* 4.2 17.0 - - + -
297A ILE* 2.9 28.0 + - + +
298A GLY 4.5 0.9 - - - +
300A ARG* 1.3 81.7 - - + +
302A GLY* 1.3 61.2 + - - +
303A LEU* 3.3 20.4 + - + +
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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