Contacts of the helix formed by residues 288 - 304 (chain A) in PDB entry 1U5Q
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 THR 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A PRO* 3.2 10.6 - - - +
287A PRO* 1.3 83.9 - - + +
289A VAL* 1.3 57.6 + - - +
290A ILE 3.5 2.0 - - - -
291A MET* 3.4 31.0 + - + -
292A ASP* 2.7 55.2 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 3.8 27.8 - - + +
127A GLU* 3.8 32.1 - - + +
130A ALA* 3.7 25.6 - - + -
285A ARG* 4.3 6.5 - - + -
286A PRO* 3.2 30.9 - - + +
287A PRO 3.4 3.2 + - - -
288A THR* 1.3 75.0 + - - +
290A ILE* 1.3 57.4 + - + +
292A ASP* 3.7 5.0 - - - +
293A LEU* 2.8 32.7 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU 5.0 0.2 - - - +
130A ALA* 3.7 32.1 - - + +
131A VAL* 4.1 23.3 - - + -
159A LEU* 4.0 17.3 - - + -
163A GLY* 3.5 36.3 - - - +
164A LEU 3.8 3.4 - - - +
165A VAL* 4.9 10.1 - - + -
287A PRO 5.2 0.6 + - - -
288A THR 3.5 0.4 - - - -
289A VAL* 1.3 72.9 - - + +
291A MET* 1.3 68.3 + - - +
293A LEU* 3.0 10.4 + - + +
294A ILE* 2.8 38.8 + - + +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 3.6 28.4 + - + +
163A GLY* 4.3 1.9 - - - -
287A PRO 5.6 0.6 + - - +
288A THR* 3.4 33.8 + - + +
290A ILE* 1.3 79.2 - - - +
292A ASP* 1.3 78.6 + - - +
294A ILE* 3.2 7.4 + - - +
295A GLN* 2.9 30.9 + - + +
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Residues in contact with ASP 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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127A GLU* 6.0 0.7 - - - +
286A PRO* 5.8 0.2 - - - +
288A THR* 2.7 45.9 + - - +
289A VAL* 3.8 5.0 - - - +
291A MET* 1.3 88.1 - - - +
293A LEU* 1.3 59.8 + - - +
295A GLN* 3.7 7.9 - - - +
296A ARG* 2.8 36.6 + - - +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.2 34.8 - - + -
119A HIS* 4.9 1.1 - - - +
123A LEU* 4.2 8.5 - - + -
127A GLU* 3.3 43.9 + - + +
131A VAL* 4.4 16.2 - - + -
159A LEU* 5.1 4.5 - - + -
289A VAL 2.8 22.1 + - - +
290A ILE* 3.0 13.9 + - + +
292A ASP* 1.3 71.9 - - - +
294A ILE* 1.3 59.8 + - + +
296A ARG* 3.2 23.0 - - - +
297A THR* 2.7 36.9 + - - +
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Residues in contact with ILE 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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109A LEU* 3.9 30.7 - - + -
115A LEU* 5.6 4.3 - - + -
159A LEU* 4.2 23.3 - - + -
160A SER 3.9 23.6 - - - +
161A GLU* 4.3 13.0 - - + +
162A PRO 4.4 4.0 - - - +
163A GLY* 4.0 6.3 - - - -
290A ILE* 2.8 36.3 + - + +
291A MET 3.5 6.1 - - - +
293A LEU* 1.3 75.3 - - + +
295A GLN* 1.3 61.3 + - - +
297A THR* 3.1 7.1 + - - -
298A LYS* 2.8 43.2 + - + +
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Residues in contact with GLN 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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291A MET* 2.9 19.6 + - + +
292A ASP* 3.2 10.1 + - - +
294A ILE* 1.3 77.3 - - - +
296A ARG* 1.3 62.5 + - - +
298A LYS* 3.3 21.7 + - - +
299A ASP* 2.5 70.5 + - - +
302A ARG* 5.3 3.3 + - - +
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS* 3.5 36.3 + - + +
122A PRO 5.1 2.0 + - - -
123A LEU* 4.3 8.3 - - - +
124A GLN* 3.5 20.9 - - - +
127A GLU* 2.7 43.4 + - - -
292A ASP* 2.8 22.0 + - - +
293A LEU* 3.2 25.6 - - - +
295A GLN* 1.3 75.0 - - - +
297A THR* 1.3 57.7 + - - +
299A ASP* 3.7 9.9 - - - +
300A ALA* 3.0 27.7 + - - +
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Residues in contact with THR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.5 30.0 - - + +
118A VAL* 4.3 20.9 - - + -
119A HIS* 3.0 25.3 + - - +
293A LEU* 2.7 23.3 + - - +
294A ILE* 3.4 7.2 - - - -
296A ARG* 1.3 75.4 - - - +
298A LYS* 1.3 66.9 + - - +
300A ALA* 3.2 2.4 + - - +
301A VAL* 3.0 26.2 + - + +
315A ILE* 4.6 14.4 - - + -
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Residues in contact with LYS 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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109A LEU* 3.8 27.4 - - + -
161A GLU* 2.9 27.8 + - - -
294A ILE* 2.8 25.9 + - + +
295A GLN* 3.8 22.5 + - - +
297A THR* 1.3 74.4 - - - +
299A ASP* 1.3 64.7 + - - +
301A VAL* 3.3 4.3 + - - +
302A ARG* 3.1 42.3 + - - +
315A ILE* 4.2 6.1 - - + +
316A LEU* 3.8 26.1 - - + +
318A GLN* 4.0 10.7 - - - +
319A GLU* 4.6 6.7 + - - +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLN* 2.5 53.6 + - - +
296A ARG* 3.7 8.6 - - - +
298A LYS* 1.3 76.1 - - - +
300A ALA* 1.3 62.9 + - - +
302A ARG* 3.3 21.8 + - - +
303A GLU* 3.1 28.6 - - - +
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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
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118A VAL* 3.7 20.6 - - + +
119A HIS* 3.7 12.8 - - + +
296A ARG 3.0 18.0 + - - +
297A THR 3.2 4.9 + - - +
299A ASP* 1.3 76.3 - - - +
301A VAL* 1.3 63.7 + - - +
303A GLU* 3.0 19.2 + - - +
304A LEU* 3.3 15.9 + - + +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.6 29.4 - - + -
297A THR 3.0 15.9 + - - +
298A LYS 3.3 6.5 + - - +
300A ALA* 1.3 75.4 - - - +
302A ARG* 1.3 62.2 + - - +
304A LEU* 3.1 28.8 + - + +
307A LEU* 3.6 23.9 - - + +
312A MET 3.4 25.8 - - - +
313A LYS* 3.9 4.7 - - - -
315A ILE* 4.2 11.4 - - + -
316A LEU* 4.0 17.0 - - + -
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Residues in contact with ARG 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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295A GLN* 5.3 2.2 + - - +
298A LYS* 3.1 34.9 + - - +
299A ASP* 3.6 20.5 + - - +
300A ALA 3.2 0.2 - - - -
301A VAL* 1.3 76.3 - - - +
303A GLU* 1.3 77.3 + - - +
304A LEU 3.6 3.1 + - - +
307A LEU* 4.3 11.8 - - - +
316A LEU* 3.5 19.0 - - + +
319A GLU* 2.7 44.6 + - - -
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Residues in contact with GLU 303 (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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299A ASP* 3.1 25.4 - - + +
300A ALA* 3.0 9.8 + - - +
302A ARG* 1.3 93.3 - - - +
304A LEU* 1.3 66.7 + - - +
305A ASP* 3.4 9.7 + - - +
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Residues in contact with LEU 304 (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* 4.9 17.3 - - + +
300A ALA* 3.3 12.8 + - + +
301A VAL* 3.1 35.5 + - + +
302A ARG 3.3 2.1 - - - +
303A GLU* 1.3 79.4 - - - +
305A ASP* 1.3 65.1 + - - +
306A ASN 3.5 1.6 + - - -
307A LEU* 3.6 16.7 + - + +
310A ARG* 3.9 43.1 - - + +
312A MET* 4.3 20.0 - - + -
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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
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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