Contacts of the helix formed by residues 296 - 316 (chain B) in PDB entry 5TWV
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 GLY 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B CYS 3.7 8.7 + - - +
293B HIS* 3.6 13.1 + - - -
294B ALA 3.2 3.7 - - - -
295B PHE* 1.3 76.1 - - - +
297B ARG* 1.3 65.1 + - - +
298B ARG 3.5 0.6 + - - -
299B LEU* 3.9 11.3 + - - +
300B ILE* 4.5 4.3 + - - +
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Residues in contact with ARG 297 (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 PHE 3.2 4.6 + - - -
296B GLY* 1.3 75.0 - - - +
298B ARG* 1.3 54.8 + - - +
299B LEU 3.2 0.5 + - - -
300B ILE* 3.7 1.7 + - - +
301B LEU* 2.7 52.2 + - + +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PHE* 4.1 8.4 + - + +
296B GLY 3.5 0.6 - - - -
297B ARG* 1.3 76.9 - - - +
299B LEU* 1.3 60.2 + - - +
301B LEU* 3.9 12.8 - - + -
302B SER* 2.9 33.8 + - - +
379B VAL* 5.1 8.7 - - + +
383B THR* 3.9 25.4 + - + +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B CYS* 5.1 8.3 - - + +
295B PHE* 4.8 16.9 - - + +
296B GLY 3.9 8.9 + - - +
297B ARG 3.2 0.8 + - - -
298B ARG* 1.3 77.2 - - - +
300B ILE* 1.3 59.4 + - - +
302B SER* 4.1 1.1 - - - -
303B SER* 2.9 28.8 + - - -
383B THR* 5.8 2.2 - - - +
432B PHE* 5.2 15.3 - - + -
436B PRO* 4.6 6.1 - - - +
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLY 4.5 3.5 + - - +
297B ARG 3.7 4.0 + - - +
299B LEU* 1.3 76.4 - - - +
301B LEU* 1.3 60.7 + - - +
303B SER* 3.7 8.3 - - - -
304B THR* 2.9 28.1 + - - -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 2.7 37.4 + - + +
298B ARG* 3.9 9.9 - - + +
300B ILE* 1.3 77.5 - - - +
302B SER* 1.3 62.1 + - - +
304B THR* 3.0 7.6 + - - -
305B PHE* 2.9 57.2 + - + -
379B VAL* 5.5 6.3 - - + -
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG 2.9 21.0 + - - -
299B LEU 4.2 0.9 - - - -
301B LEU* 1.3 74.4 - - - +
303B SER* 1.3 60.7 + - - +
305B PHE* 3.5 6.7 + - - +
306B ARG* 2.9 18.0 + - - +
376B SER* 2.5 45.1 + - - +
379B VAL* 4.2 16.8 - - - -
380B ALA* 5.0 3.4 - - - -
436B PRO* 4.4 8.5 - - - -
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU 2.9 20.1 + - - -
300B ILE* 3.7 9.9 - - - -
302B SER* 1.3 78.8 - - - +
304B THR* 1.3 56.1 + - - +
306B ARG* 3.2 3.5 + - - +
307B ILE* 2.9 27.1 + - - +
436B PRO* 3.8 23.2 - - - +
439B TRP* 4.4 22.9 - - - -
440B THR* 5.5 0.9 - - - -
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Residues in contact with THR 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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300B ILE 2.9 19.6 + - - -
301B LEU* 3.0 7.4 + - - -
303B SER* 1.3 76.1 - - - +
305B PHE* 1.3 60.5 + - - +
307B ILE* 3.2 8.9 + - - +
308B LEU* 2.9 26.9 + - - +
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Residues in contact with PHE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 2.9 55.7 + - + -
302B SER* 3.8 7.4 - - - +
304B THR* 1.3 75.1 - - - +
306B ARG* 1.3 58.4 + - - +
308B LEU* 3.3 9.9 + - + +
309B ALA* 2.9 26.9 + - - +
372B PHE* 4.2 24.1 - - + +
375B ALA* 5.7 4.7 - - + -
376B SER* 4.1 16.6 - - - -
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER 2.9 15.8 + - - +
303B SER 3.4 9.6 - - - +
304B THR 3.2 0.2 - - - -
305B PHE* 1.3 76.9 - - - +
307B ILE* 1.3 57.5 + - - +
309B ALA* 3.3 9.2 + - - +
310B ASP* 2.9 24.9 + - - +
373B LEU* 6.0 0.9 - - - +
376B SER* 4.0 10.9 + - - +
377B TYR* 6.5 0.4 - - + -
436B PRO* 4.2 24.7 - - + +
437B ASN* 5.2 1.3 - - - +
440B THR* 4.2 9.8 - - - -
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER 2.9 14.2 + - - +
304B THR* 3.2 10.9 + - - +
306B ARG* 1.3 74.1 - - - +
308B LEU* 1.3 62.0 + - - +
310B ASP* 3.2 10.4 + - - +
311B LEU* 2.9 24.4 + - - +
439B TRP* 6.2 3.1 - - + -
440B THR* 4.7 6.0 - - - -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR 2.9 13.6 + - - +
305B PHE* 3.6 16.6 - - + +
307B ILE* 1.3 77.0 - - - +
309B ALA* 1.3 58.0 + - - +
311B LEU* 3.1 9.6 + - - +
312B LEU* 2.9 29.5 + - - +
372B PHE* 5.4 5.2 - - + -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE 2.9 13.8 + - - +
306B ARG* 3.4 13.0 - - - +
307B ILE 3.2 0.2 - - - -
308B LEU* 1.3 76.7 - - - +
310B ASP* 1.3 57.9 + - - +
313B GLY* 2.9 27.7 + - - -
369B GLN* 3.8 30.6 - - - +
372B PHE* 4.6 3.3 - - - +
373B LEU* 4.2 17.7 - - + +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ARG 2.9 14.4 + - - +
307B ILE* 3.2 13.9 + - - +
309B ALA* 1.3 75.2 - - - +
311B LEU* 1.3 59.6 + - - +
314B PHE* 3.0 33.6 + - - +
440B THR* 4.7 17.7 - - - +
443B VAL* 5.5 6.1 - - + -
444B GLN* 4.9 15.0 - - + +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE 2.9 12.8 + - - +
308B LEU* 3.1 13.4 + - - +
310B ASP* 1.3 80.5 - - - +
312B LEU* 1.3 62.8 + - - +
314B PHE* 3.9 4.3 + - - +
315B ALA* 4.0 13.0 + - - +
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Residues in contact with LEU 312 (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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308B LEU 2.9 14.1 + - - +
311B LEU* 1.3 78.6 - - - +
313B GLY* 1.3 62.7 + - - +
315B ALA* 4.0 3.5 + - - +
316B GLY* 3.9 12.0 + - - -
365B ALA* 3.7 34.4 - - + +
366B LEU* 5.8 0.7 - - - -
368B LEU* 5.0 5.2 - - + -
369B GLN* 3.7 14.6 - - + +
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Residues in contact with GLY 313 (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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309B ALA 2.9 18.6 + - - -
310B ASP* 5.1 0.2 - - - -
312B LEU* 1.3 76.9 - - - +
314B PHE* 1.3 62.7 + - - +
316B GLY* 3.5 12.4 + - - -
317B PRO* 4.7 2.3 - - - +
369B GLN* 3.8 11.1 - - - +
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Residues in contact with PHE 314 (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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310B ASP* 3.0 22.9 + - + +
311B LEU 4.4 2.2 - - - +
312B LEU 3.5 0.4 - - - -
313B GLY* 1.3 77.0 - - - +
315B ALA* 1.3 63.1 + - - +
316B GLY 3.4 0.3 + - - -
317B PRO* 3.6 9.5 - - - +
444B GLN* 5.7 9.4 - - + +
447B VAL* 5.1 15.5 - - + -
448B GLY* 5.7 5.4 - - - +
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Residues in contact with ALA 315 (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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311B LEU 4.0 11.4 + - - +
312B LEU 4.0 4.8 + - - +
313B GLY 3.4 0.8 - - - -
314B PHE* 1.3 78.4 - - - +
316B GLY* 1.3 54.4 + - - +
317B PRO* 2.4 22.1 - - - +
318B LEU* 2.7 27.7 + - + +
319B CYS 5.4 0.2 - - - -
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU 3.9 7.1 + - - -
313B GLY 3.5 10.1 + - - -
314B PHE 3.3 2.2 - - - -
315B ALA* 1.3 75.1 - - - +
317B PRO* 1.3 65.0 - - - +
318B LEU 3.5 0.9 + - - -
319B CYS* 3.9 14.7 + - - +
320B ILE* 4.3 2.9 + - - +
362B LEU* 4.9 10.8 - - - +
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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