Contacts of the helix formed by residues 295 - 312 (chain B) in PDB entry 4M5X
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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224B TYR* 3.7 14.6 + - - -
294B HIS* 1.3 76.5 - - - +
296B VAL* 1.3 64.8 + - - +
297B GLN* 3.1 34.0 + - - +
298B GLU* 2.9 45.8 + - - +
299B LEU 3.2 9.2 + - - -
407B MET* 6.0 1.0 - - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TYR* 3.8 41.3 - - + -
228B LEU* 4.3 15.0 - - + -
295B ASP* 1.3 76.7 - - + +
297B GLN* 1.3 69.2 + - - +
299B LEU* 3.4 2.1 + - - +
300B CYS* 3.0 27.8 + - - +
405B GLN* 3.9 10.1 - - + -
454B LEU* 4.2 12.6 - - + -
514B TYR* 3.9 18.8 - - + -
515B MET* 3.8 31.9 - - - -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP* 3.1 33.9 + - - +
296B VAL* 1.3 80.8 + - - +
298B GLU* 1.3 55.9 + - + +
300B CYS* 3.5 7.4 + - - +
301B ARG* 2.9 54.6 + - - +
349B ASP* 4.0 13.1 - - - +
351B GLN* 3.7 24.2 - - - +
405B GLN* 3.4 38.3 - - - +
407B MET* 4.6 12.5 - - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TRP* 4.5 2.2 - - + -
293B GLN 4.5 0.9 - - - +
294B HIS* 3.2 30.4 - - + +
295B ASP* 2.9 46.7 + - - +
297B GLN* 1.3 75.0 - - + +
299B LEU* 1.3 65.8 + - - +
301B ARG* 3.1 21.9 + - - +
302B VAL* 2.9 28.1 + - + +
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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
----------------------------------------------------------
224B TYR* 3.7 39.3 - - + -
225B MET* 3.9 28.3 - - + -
228B LEU* 3.9 17.3 - - + -
283B PHE* 3.6 32.1 - - + -
285B TRP* 3.8 20.7 - - + -
291B PHE* 4.2 2.0 - - + -
295B ASP 3.2 4.0 + - - -
296B VAL 3.7 4.0 - - - +
298B GLU* 1.3 78.7 - - - +
300B CYS* 1.3 63.4 + - - +
302B VAL* 3.0 5.4 + - + +
303B LEU* 2.9 34.4 + - + +
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Residues in contact with CYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 3.7 25.3 - - + +
232B LEU* 4.6 5.2 - - - -
296B VAL 3.0 18.1 + - - +
297B GLN* 3.7 8.7 - - - +
299B LEU* 1.3 76.5 - - - +
301B ARG* 1.3 58.0 + - + +
303B LEU* 3.4 3.0 + - - +
304B LEU* 2.9 62.2 + - - +
349B ASP* 5.7 3.4 - - - +
403B HIS* 3.9 28.3 - - - -
405B GLN* 5.9 2.2 - - - +
515B MET* 5.6 1.1 - - + -
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLN* 2.9 34.7 + - - +
298B GLU* 3.1 18.1 + - - +
300B CYS* 1.3 75.5 - - - +
302B VAL* 1.3 59.4 + - + +
304B LEU* 4.8 3.8 - - - -
305B ASP* 2.9 46.3 + - - +
348B TYR* 6.2 3.1 - - + +
349B ASP* 3.2 37.9 + - - +
351B GLN* 3.6 18.4 + - - +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 5.6 0.2 - - + -
283B PHE* 4.0 33.7 - - + -
285B TRP* 4.2 19.7 - - + +
298B GLU* 2.9 18.3 + - + +
299B LEU* 3.0 10.3 + - + +
301B ARG* 1.3 76.6 - - + +
303B LEU* 1.3 65.7 + - + +
305B ASP* 4.2 3.1 - - - +
306B ASN* 2.8 43.1 + - - +
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Residues in contact with LEU 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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225B MET* 6.0 0.2 - - + -
228B LEU* 4.0 26.7 - - + -
229B LEU* 4.2 17.9 - - + -
232B LEU* 4.1 20.2 - - + -
256B VAL* 4.3 13.0 - - + +
260B LEU* 4.9 14.4 - - + -
279B LEU* 4.4 9.4 - - + -
283B PHE* 3.9 33.4 - - + -
299B LEU* 2.9 26.1 + - + +
300B CYS 4.0 2.7 - - - +
302B VAL* 1.3 76.2 - - - +
304B LEU* 1.3 63.6 + - + +
306B ASN* 3.4 5.5 + - - +
307B VAL* 3.1 28.0 + - - +
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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
----------------------------------------------------------
232B LEU* 4.6 11.7 - - + -
238B LEU* 4.2 17.0 - - + -
260B LEU* 6.4 1.8 - - + -
300B CYS* 2.9 42.8 + - - +
301B ARG* 4.3 3.1 - - - +
303B LEU* 1.3 76.0 - - + +
305B ASP* 1.3 61.8 + - - +
307B VAL* 3.2 8.8 - - + +
308B GLU* 2.8 32.7 + - - +
320B ILE* 4.1 22.5 - - + +
324B PHE* 4.1 41.7 - - + -
348B TYR* 5.9 5.6 - - + -
403B HIS* 5.1 0.4 - - + +
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ARG* 2.9 33.1 + - - +
302B VAL* 4.2 3.6 - - - +
304B LEU* 1.3 77.2 - - - +
306B ASN* 1.3 59.0 + - - +
308B GLU* 4.0 5.3 - - - +
309B ASN* 2.8 43.7 + - - +
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Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 3.6 40.0 + - + +
257B PRO* 4.1 12.4 - - + +
283B PHE* 5.2 0.8 - - - +
302B VAL* 2.8 38.7 + - - +
303B LEU 3.5 4.5 - - - +
304B LEU 3.2 0.2 - - - -
305B ASP* 1.3 77.2 - - - +
307B VAL* 1.3 65.9 + - + +
309B ASN* 3.4 7.9 + - - +
310B LYS* 3.1 22.0 + - - +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LEU* 4.8 1.1 - - + -
242B VAL* 4.2 7.6 - - + -
245B MET* 3.9 27.8 - - + -
256B VAL* 5.6 1.6 - - + -
257B PRO* 4.7 8.3 - - + -
260B LEU* 3.8 27.1 - - + -
303B LEU 3.1 14.3 + - - +
304B LEU* 3.2 21.8 - - + +
306B ASN* 1.3 73.4 - - + +
308B GLU* 1.3 70.8 + - - +
310B LYS* 2.9 12.6 + - - +
311B MET* 3.0 25.3 + - + +
320B ILE* 3.6 20.6 - - + -
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU 2.8 19.2 + - - +
305B ASP* 4.0 5.4 - - - +
307B VAL* 1.3 76.9 - - - +
309B ASN* 1.3 63.9 + - - +
311B MET* 3.1 13.3 + - - +
312B LYS* 3.4 35.4 + - - +
317B GLU* 4.6 2.1 - - - +
318B GLY* 3.2 23.4 + - - -
319B THR 3.9 3.3 + - - -
320B ILE* 3.1 43.3 + - + +
321B PRO* 3.7 16.0 - - + +
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Residues in contact with ASN 309 (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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305B ASP* 2.8 32.4 + - - +
306B ASN* 3.7 6.8 - - - +
307B VAL 3.2 0.2 - - - -
308B GLU* 1.3 78.7 - - - +
310B LYS* 1.3 60.1 + - - +
311B MET 3.4 0.5 + - - -
312B LYS* 3.6 36.8 + - - +
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Residues in contact with LYS 310 (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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245B MET* 3.8 23.8 - - + -
246B PRO* 3.4 41.6 + - + +
247B THR* 4.0 3.1 - - - -
250B ASP* 2.8 37.3 + - - -
257B PRO* 3.8 21.5 - - + -
306B ASN 3.1 11.8 + - - +
307B VAL 2.9 9.6 + - - +
309B ASN* 1.3 76.8 - - - +
311B MET* 1.3 60.6 + - - +
312B LYS 3.6 2.3 + - - +
314B THR* 3.9 3.6 - - - +
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Residues in contact with MET 311 (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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238B LEU* 4.7 0.9 - - + +
241B ALA* 3.6 38.4 - - + +
242B VAL* 3.8 17.5 - - + +
245B MET* 3.8 15.9 - - + +
307B VAL* 3.0 14.6 + - + +
308B GLU* 3.1 9.3 + - - +
310B LYS* 1.3 77.3 - - - +
312B LYS* 1.3 65.2 + - - +
314B THR* 2.5 31.4 + - - +
316B VAL* 3.5 36.1 - - + +
317B GLU* 3.4 11.4 - - - +
319B THR* 4.0 4.5 - - - -
320B ILE* 3.8 30.7 - - + -
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Residues in contact with LYS 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 GLU* 3.4 34.5 + - - +
309B ASN* 3.7 32.8 - - - +
310B LYS 3.4 4.0 - - - +
311B MET* 1.3 78.0 - - - +
313B GLY* 1.3 60.7 + - - +
314B THR* 3.7 5.2 - - - +
317B GLU* 3.8 20.1 + - - +
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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