Contacts of the helix formed by residues 288 - 304 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B PRO* 4.1 10.7 - - - +
287B PRO* 1.3 87.7 - - + +
289B VAL* 1.3 54.0 + - - +
290B ILE 3.4 2.2 - - - -
291B MET* 3.2 29.4 + - + +
292B ASP* 2.7 60.1 + - - +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 4.0 20.9 - - + +
127B GLU* 3.8 39.4 - - + +
130B ALA* 4.0 12.8 - - + -
285B ARG* 4.1 5.2 - - + -
286B PRO* 3.0 44.8 - - + +
287B PRO 3.4 2.6 - - - -
288B THR* 1.3 76.2 + - - +
290B ILE* 1.3 59.2 + - + +
292B ASP* 3.4 4.4 + - - +
293B LEU* 2.9 28.3 + - + +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU 4.9 0.4 - - - +
130B ALA* 3.7 28.9 - - + -
131B VAL* 3.9 17.7 - - + -
159B LEU* 3.9 21.5 - - + -
163B GLY* 3.6 34.8 - - - +
164B LEU 3.9 1.3 - - - +
165B VAL* 3.6 25.6 - - + -
287B PRO 5.1 1.0 + - - -
288B THR 3.4 0.4 - - - -
289B VAL* 1.3 72.8 - - + +
291B MET* 1.3 61.2 + - - +
293B LEU* 3.2 11.0 + - + +
294B ILE* 2.9 33.8 + - + +
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Residues in contact with MET 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO* 3.3 32.5 + - + +
163B GLY* 4.3 1.9 - - - -
287B PRO 5.6 0.2 - - - +
288B THR* 3.5 34.1 - - + +
290B ILE* 1.3 80.5 - - - +
292B ASP* 1.3 63.8 + - - +
294B ILE* 3.2 7.7 + - - +
295B GLN* 2.9 30.6 + - + +
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLU* 6.0 0.4 - - - +
288B THR* 2.7 51.6 + - - +
289B VAL* 3.7 4.7 - - - +
291B MET* 1.3 78.7 - - - +
293B LEU* 1.3 60.3 + - - +
295B GLN* 3.5 7.3 - - - +
296B ARG* 2.8 35.2 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.4 29.4 - - + -
119B HIS* 4.9 1.3 - - + +
123B LEU* 4.2 13.2 - - + -
127B GLU* 3.4 46.4 + - + +
131B VAL* 4.4 16.2 - - + -
159B LEU* 5.1 3.8 - - + -
289B VAL 2.9 18.6 + - - +
290B ILE* 3.2 13.0 + - + +
292B ASP* 1.3 73.8 - - - +
294B ILE* 1.3 60.3 + - + +
296B ARG* 3.4 21.1 - - - +
297B THR* 2.6 41.2 + - - +
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.0 28.7 - - + -
115B LEU* 5.6 3.4 - - + -
159B LEU* 4.3 22.0 - - + -
160B SER 3.8 29.4 - - - +
161B GLU* 4.1 15.9 - - + +
162B PRO 4.6 2.9 - - - +
163B GLY* 4.2 11.9 - - - +
290B ILE* 2.9 25.4 + - + +
291B MET* 3.5 6.1 - - - +
293B LEU* 1.3 75.1 - - + +
295B GLN* 1.3 66.6 + - - +
297B THR* 3.0 8.3 + - - -
298B LYS* 2.9 35.4 + - - +
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Residues in contact with GLN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B MET* 2.9 17.3 + - + +
292B ASP* 3.5 8.3 - - - +
294B ILE* 1.3 79.1 - - - +
296B ARG* 1.3 62.7 + - - +
297B THR 3.2 0.2 + - - -
298B LYS* 3.2 20.4 + - - +
299B ASP* 2.9 60.5 + - - +
302B ARG* 5.5 2.6 - - - +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B HIS* 3.5 37.9 + - - +
122B PRO 5.0 2.8 + - - -
123B LEU* 4.5 9.3 - - - +
124B GLN* 3.7 17.5 - - - +
127B GLU* 2.8 40.9 + - - -
292B ASP 2.8 20.2 + - - +
293B LEU* 3.4 21.6 - - - +
295B GLN* 1.3 75.5 - - - +
297B THR* 1.3 62.7 + - - +
299B ASP* 3.7 10.9 - - - +
300B ALA* 3.2 22.2 + - - +
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Residues in contact with THR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP 5.6 0.2 - - - -
115B LEU* 3.4 31.8 - - + +
118B VAL* 4.0 26.9 - - + -
119B HIS* 3.1 20.6 + - - +
293B LEU* 2.6 24.1 + - - +
294B ILE* 3.0 6.2 + - - -
296B ARG* 1.3 76.5 - - - +
298B LYS* 1.3 65.3 + - - +
300B ALA* 3.3 2.4 + - - +
301B VAL* 3.0 26.0 + - + +
315B ILE* 4.8 13.2 - - + -
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.8 20.0 - - + -
161B GLU* 2.7 41.5 + - - -
294B ILE* 2.9 20.9 + - + +
295B GLN* 3.2 24.7 + - - +
297B THR* 1.3 76.3 - - - +
299B ASP* 1.3 62.5 + - - +
301B VAL* 3.1 15.3 + - - +
302B ARG* 3.1 35.5 + - - +
315B ILE* 4.5 5.6 - - + -
316B LEU* 4.2 19.5 - - + +
318B GLN* 3.8 9.9 - - - +
319B GLU* 4.4 7.5 + - - +
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Residues in contact with ASP 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLN* 2.9 44.8 + - - +
296B ARG* 3.7 10.2 - - - +
298B LYS* 1.3 79.0 - - - +
300B ALA* 1.3 63.6 + - - +
302B ARG* 3.2 27.9 + - - +
303B GLU* 3.4 15.9 - - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 3.7 12.1 - - + +
119B HIS* 3.6 20.9 - - + +
296B ARG 3.2 15.3 + - - +
297B THR 3.6 4.7 - - - +
298B LYS 3.2 0.2 - - - -
299B ASP* 1.3 80.1 - - - +
301B VAL* 1.3 63.3 + - - +
303B GLU* 3.0 19.3 + - - +
304B LEU* 3.3 15.2 + - + +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 3.7 28.0 - - + -
297B THR* 3.0 18.6 + - + +
298B LYS* 3.1 8.3 + - - +
300B ALA* 1.3 75.0 - - - +
302B ARG* 1.3 63.1 + - - +
304B LEU* 3.1 29.3 + - + +
307B LEU* 3.7 12.4 - - + +
312B MET 3.6 24.0 - - - +
313B LYS* 4.0 10.1 - - - -
315B ILE* 4.1 11.7 - - + -
316B LEU* 3.9 25.4 - - + -
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B GLN* 5.5 2.0 - - - +
298B LYS* 3.1 29.2 + - - +
299B ASP* 3.2 18.6 + - - +
301B VAL* 1.3 76.8 - - - +
303B GLU* 1.3 66.5 + - + +
304B LEU 3.6 4.2 + - - +
307B LEU* 4.6 10.5 - - - +
316B LEU* 3.7 25.8 - - + +
319B GLU* 2.8 44.0 + - - -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP 3.4 16.2 - - - +
300B ALA* 3.0 11.0 + - - +
302B ARG* 1.3 82.1 - - - +
304B LEU* 1.3 67.7 + - - +
305B ASP* 3.4 10.4 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 4.8 18.4 - - + +
300B ALA* 3.3 11.2 + - + +
301B VAL* 3.1 32.9 + - + +
302B ARG 4.2 2.3 - - - +
303B GLU* 1.3 80.0 - - - +
305B ASP* 1.3 63.5 + - - +
306B ASN 3.6 1.7 + - - -
307B LEU* 3.7 16.8 + - + +
310B ARG* 4.0 43.7 - - + +
312B MET* 4.1 26.5 - - + -
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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
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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