Contacts of the helix formed by residues 295 - 311 (chain B) in PDB entry 4U1D
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 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B PHE* 3.2 20.8 + - + +
293B SER* 3.3 16.3 - - - +
294B GLY* 1.3 82.0 - - - +
296B PRO* 1.3 66.2 - - - +
297B LEU 3.3 2.4 + - - -
298B LEU* 3.4 22.0 + - + +
299B HIS 3.1 17.0 + - - -
346B ASP* 4.1 12.4 - - - +
348B HIS* 2.7 39.2 + - - +
352B TYR* 4.6 9.0 + - - +
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Residues in contact with PRO 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE 5.0 0.4 - - - +
294B GLY 3.3 12.3 - - - +
295B ASP* 1.3 83.0 - - - +
297B LEU* 1.3 69.4 + - + +
299B HIS* 3.4 12.0 - - + +
300B THR* 3.0 29.1 + - - -
331B SER 4.9 2.1 - - - +
334B SER 5.7 1.1 - - - +
335B THR* 3.9 32.6 + - + +
336B GLN* 4.6 18.4 - - + +
352B TYR* 5.4 1.8 - - - +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP 3.3 0.2 - - - -
296B PRO* 1.3 82.3 - - + +
298B LEU* 1.3 64.3 + - - +
300B THR* 3.5 2.1 + - - +
301B THR* 3.0 27.6 + - - -
335B THR* 3.9 26.5 - - + +
338B ASP* 4.5 9.0 - - - +
352B TYR* 3.8 16.2 - - + +
360B LYS* 4.4 18.2 - - - -
361B PRO* 3.1 33.4 - - + +
362B THR 4.2 2.7 - - - +
363B ARG* 4.1 17.9 - - - -
366B MET* 3.6 28.8 - - + +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 3.5 43.6 - - + -
295B ASP* 3.4 20.5 + - + +
296B PRO 3.3 0.2 - - - -
297B LEU* 1.3 74.2 - - - +
299B HIS* 1.3 66.3 + - - +
301B THR* 3.2 5.9 + - - +
302B ALA* 2.9 25.6 + - - +
348B HIS* 4.5 3.6 - - + +
351B MET* 3.7 23.8 - - + -
352B TYR* 3.5 48.0 + - + +
355B LEU* 4.0 22.0 - - + +
357B LEU* 5.2 1.6 - - + -
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 2.8 31.9 + - + +
290B PHE* 3.7 16.3 - - + +
291B PHE* 3.8 27.1 - + + +
295B ASP 3.1 14.3 + - - +
296B PRO* 3.4 14.8 - - + +
298B LEU* 1.3 76.8 - - - +
300B THR* 1.3 62.5 + - - +
302B ALA* 3.4 4.6 + - - +
303B TRP* 3.1 46.3 + + - -
331B SER* 3.9 14.4 - - - -
419B GLN* 5.4 2.0 - - - -
420B TYR* 2.6 31.8 + + - -
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO 3.0 15.9 + - - -
297B LEU* 4.0 4.5 - - - -
298B LEU 3.3 0.4 - - - -
299B HIS* 1.3 73.9 - - - +
301B THR* 1.3 68.1 + - - +
303B TRP* 3.3 6.8 + - - +
304B LYS* 3.0 23.0 + - + +
328B ILE* 3.6 17.5 - - + +
331B SER* 2.8 38.4 + - - +
332B ALA* 4.1 4.0 + - + -
335B THR* 4.4 1.4 + - - -
366B MET* 4.1 18.8 - - + -
370B ILE* 3.9 19.1 - - + -
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU 3.0 16.9 + - - -
298B LEU* 3.2 9.9 + - - -
300B THR* 1.3 76.1 - - - +
302B ALA* 1.3 56.5 + - - +
304B LYS* 3.0 15.1 + - + +
305B LYS* 2.9 36.8 + - + +
355B LEU* 3.5 26.5 - - + -
357B LEU* 4.0 31.3 - - + +
366B MET* 3.4 16.4 - - - +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TYR* 3.9 8.0 - - - +
286B LEU* 3.7 31.0 - - + -
287B VAL* 3.5 21.5 - - + +
290B PHE* 4.6 1.8 - - + -
298B LEU 2.9 16.4 + - - +
299B HIS 3.7 1.6 - - - +
301B THR* 1.3 77.9 - - - +
303B TRP* 1.3 62.2 + - - +
305B LYS* 3.3 11.2 + - - +
306B PHE* 3.0 23.7 + - - +
355B LEU* 5.1 2.2 - - + -
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Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 6.4 2.0 - - + -
287B VAL* 3.4 23.5 - - + +
299B HIS* 3.1 55.1 + + - -
300B THR* 3.4 12.6 - - - +
302B ALA* 1.3 74.8 - - - +
304B LYS* 1.3 59.4 + - - +
306B PHE* 3.2 22.1 + + - +
307B TYR* 2.9 28.7 + - + +
324B TYR* 4.0 42.4 - + + -
327B THR* 3.4 30.7 - - + +
328B ILE* 3.8 26.4 - - + +
331B SER* 5.0 2.0 - - - -
419B GLN* 5.4 5.0 - - - +
420B TYR* 4.1 0.8 + - - -
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 3.0 18.8 + - + +
301B THR* 3.0 11.4 + - - +
303B TRP* 1.3 74.8 - - - +
305B LYS* 1.3 61.3 + - - +
307B TYR* 3.1 2.6 + - - +
308B LYS* 2.8 32.8 + - - +
328B ILE* 3.7 24.9 - - + -
366B MET* 3.5 24.5 - - - +
369B SER* 2.9 33.2 + - - -
370B ILE* 4.1 14.1 - - + -
373B ASP* 6.1 0.2 - - - -
376B ILE* 4.1 18.8 - - + +
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLY 6.0 0.6 + - - -
283B TYR* 3.6 53.1 + - + -
301B THR* 2.9 29.5 + - + +
302B ALA* 3.6 9.0 - - - +
304B LYS* 1.3 76.4 - - - +
306B PHE* 1.3 61.2 + - - +
308B LYS* 4.1 7.2 - - + +
309B LEU* 3.3 23.2 + - - +
355B LEU* 3.5 36.1 + - + +
356B ASN* 5.0 7.5 - - - +
357B LEU* 5.0 1.8 - - - -
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 3.2 38.1 - - + -
283B TYR* 4.0 13.0 - - + +
284B GLU* 3.2 43.5 - - + +
287B VAL* 5.4 1.1 - - + -
302B ALA 3.0 12.8 + - - +
303B TRP* 3.5 27.8 - + - +
304B LYS 3.1 0.2 - - - -
305B LYS* 1.3 76.5 - - - +
307B TYR* 1.3 58.6 + - - +
309B LEU* 3.3 4.5 + - - -
310B TYR* 2.7 55.7 + + + +
324B TYR* 3.9 30.1 - + - -
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Residues in contact with TYR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TRP* 2.9 17.0 + - + +
304B LYS* 3.1 4.2 + - - +
306B PHE* 1.3 78.8 - - + +
308B LYS* 1.3 63.7 + - - +
310B TYR* 3.7 4.1 - + - +
311B SER* 2.9 40.6 + - - -
321B PHE* 3.1 40.6 - + - +
324B TYR* 3.8 30.7 - + + -
325B SER* 2.9 27.8 + - - -
328B ILE* 3.6 16.8 - - + -
375B SER* 3.0 31.7 + - - -
376B ILE* 3.6 25.1 - - + -
379B LYS* 3.8 4.2 - - - +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A SER 5.0 4.0 + - - -
344A GLY* 3.7 31.3 - - - +
304B LYS 2.8 16.6 + - - +
305B LYS* 4.1 6.7 - - + +
307B TYR* 1.3 80.6 - - + +
309B LEU* 1.3 58.1 + - - +
311B SER* 2.9 19.5 + - - +
312B THR* 3.7 11.3 - - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 3.7 30.5 - - + -
344A GLY 5.1 4.9 - - - +
276B PRO* 4.0 19.0 - - + +
279B LEU* 3.8 18.6 - - + -
280B ALA* 3.4 42.6 - - + +
283B TYR* 4.0 12.3 - - + -
305B LYS 3.3 12.7 + - - +
306B PHE* 3.3 4.0 + - - +
307B TYR 3.1 0.4 - - - -
308B LYS* 1.3 77.6 - - - +
310B TYR* 1.3 59.7 + - - +
311B SER 3.2 2.2 - - - -
312B THR* 3.2 27.0 + - + +
313B ASN* 5.2 0.9 - - - +
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Residues in contact with TYR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 5.8 2.7 - - + -
306B PHE* 2.7 46.0 + + + +
307B TYR* 3.1 6.0 + + - +
309B LEU* 1.3 74.2 - - - +
311B SER* 1.3 57.2 + - - +
312B THR 3.0 9.8 + - - -
313B ASN* 3.3 36.4 + - + +
315B ARG* 3.6 14.5 + - - -
316B ALA* 3.5 29.8 - - + +
320B GLU* 2.4 41.3 + - + -
321B PHE* 4.7 11.0 - + - -
324B TYR* 3.8 27.1 - + - -
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 2.9 21.0 + - - -
308B LYS* 2.9 27.6 + - - +
310B TYR* 1.3 76.6 - - - +
312B THR* 1.3 61.3 + - - +
313B ASN 3.6 1.8 - - - -
321B PHE* 3.6 29.4 - - - -
375B SER* 6.0 3.9 - - - -
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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
------------------------------------------------------------
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