Contacts of the helix formed by residues 312 - 327 (chain A) in PDB entry 5XFR
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 PRO 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ASP* 3.2 10.0 - - - +
311A THR* 1.3 87.4 - - + +
313A LYS* 1.3 66.2 + - - +
314A SER* 4.3 9.6 - - - +
315A GLU* 2.9 41.9 + - + +
316A ARG* 3.2 10.7 + - - +
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Residues in contact with LYS 313 (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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293A MET* 5.0 0.7 - - - +
297A ASN* 3.6 43.8 + - - +
311A THR 3.6 1.8 + - - -
312A PRO* 1.3 70.7 - - - +
314A SER* 1.3 61.5 + - - +
315A GLU 3.3 0.7 + - - -
316A ARG* 3.3 40.1 + - - +
317A TYR* 4.3 3.1 + - - +
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PRO* 4.3 9.9 - - - +
313A LYS* 1.3 79.0 - - - +
315A GLU* 1.3 61.1 + - - +
316A ARG 3.4 0.4 + - - -
317A TYR* 4.4 8.5 + - - +
318A GLU* 4.9 2.8 + - - +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 4.0 7.1 - - + +
312A PRO* 2.9 36.1 + - + +
314A SER* 1.3 80.0 + - - +
316A ARG* 1.3 65.8 + - - +
317A TYR 3.3 1.3 - - - -
318A GLU* 3.3 26.1 + - - +
319A HIS* 3.2 37.6 + - + -
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Residues in contact with ARG 316 (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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266A TRP* 4.2 10.2 - - + -
293A MET* 3.6 12.6 - - + -
297A ASN* 3.1 30.3 + - - +
300A TRP* 3.3 64.9 - - + +
309A ALA 4.7 1.2 + - - -
311A THR* 3.0 34.8 + - + -
312A PRO* 3.2 8.9 + - - +
313A LYS* 3.3 34.6 + - - +
315A GLU* 1.3 77.8 - - - +
317A TYR* 1.3 57.8 + - - +
319A HIS* 3.2 5.4 + - - +
320A VAL* 3.0 31.4 + - - +
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Residues in contact with TYR 317 (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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288A SER* 3.1 41.5 + - - -
289A GLU* 3.5 33.2 + - + +
293A MET* 3.5 35.6 - - + +
313A LYS 4.3 3.6 + - - +
314A SER 4.4 6.5 + - - +
315A GLU 3.3 0.8 - - - -
316A ARG* 1.3 76.6 - - - +
318A GLU* 1.3 61.2 + - - +
320A VAL* 4.3 4.5 - - + -
321A LEU* 2.9 64.1 + - + +
342A HIS* 5.6 1.2 - - - +
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Residues in contact with GLU 318 (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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314A SER 4.9 2.1 + - - +
315A GLU* 3.3 27.9 + - - +
316A ARG 3.2 0.6 - - - -
317A TYR* 1.3 80.2 - - - +
319A HIS* 1.3 78.3 + - + +
321A LEU* 4.0 4.0 - - - +
322A GLU* 3.2 48.1 + - - +
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Residues in contact with HIS 319 (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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266A TRP* 3.4 54.0 - + + +
311A THR* 4.6 1.1 - - + +
315A GLU* 3.2 50.9 + - + +
316A ARG 3.2 4.2 + - - +
318A GLU* 1.3 92.4 + - + +
320A VAL* 1.3 61.4 + - - +
322A GLU* 3.9 12.2 - - - +
323A ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 320 (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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266A TRP* 4.1 20.9 - - + +
269A ILE* 5.1 2.7 - - + -
270A ALA* 4.4 9.4 - - + -
288A SER 5.3 0.7 - - - +
292A LEU* 4.1 18.2 - - + -
293A MET* 3.9 18.4 - - + -
296A ILE* 3.9 33.9 - - + -
316A ARG 3.0 21.7 + - - +
317A TYR* 3.9 7.2 - - + +
319A HIS* 1.3 75.2 - - - +
321A LEU* 1.3 60.5 + - - +
323A ALA* 3.2 7.1 + - - +
324A LEU* 3.0 32.8 + - + +
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Residues in contact with LEU 321 (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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288A SER* 4.1 16.2 - - - +
317A TYR* 2.9 53.6 + - + +
318A GLU* 4.0 4.5 - - - +
320A VAL* 1.3 77.9 - - - +
322A GLU* 1.3 60.5 + - + +
324A LEU* 3.3 9.8 + - + +
325A ASN* 2.7 48.4 + - - +
342A HIS* 6.0 1.6 - - + -
344A PHE* 4.6 7.2 - - + -
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Residues in contact with GLU 322 (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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318A GLU* 3.2 38.3 + - - +
319A HIS* 3.9 13.1 - - - +
320A VAL 3.3 0.2 - - - -
321A LEU* 1.3 77.1 - - + +
323A ALA* 1.3 54.3 - - - +
325A ASN* 3.1 6.0 + - - +
326A ASP* 2.7 54.6 + - - +
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Residues in contact with ALA 323 (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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266A TRP* 4.0 9.4 - - + +
267A VAL* 3.8 37.7 - - + +
270A ALA* 4.7 4.3 - - + -
319A HIS 3.0 19.2 + - - +
320A VAL* 3.2 6.5 + - - +
322A GLU* 1.3 76.8 - - - +
324A LEU* 1.3 61.1 + - - +
326A ASP* 4.5 3.8 - - - +
327A TYR* 3.1 20.4 + - - +
331A PHE* 3.3 12.8 - - - -
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Residues in contact with LEU 324 (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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270A ALA* 4.2 5.6 - - + -
274A LEU* 4.0 9.4 - - + -
288A SER* 3.8 25.1 - - - -
292A LEU* 3.7 32.8 - - + -
317A TYR* 5.9 0.2 - - + -
320A VAL* 3.0 24.4 + - + +
321A LEU* 3.5 12.3 - - - +
322A GLU 3.2 0.2 - - - -
323A ALA* 1.3 77.3 - - - +
325A ASN* 1.3 59.7 + - - +
327A TYR 4.3 3.3 - - - +
328A LYS* 5.3 0.7 - - - +
331A PHE* 3.4 50.0 - - + +
344A PHE* 3.6 36.4 - - + -
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Residues in contact with ASN 325 (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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321A LEU* 2.7 45.8 + - - +
322A GLU* 3.1 6.7 + - - +
324A LEU* 1.3 78.8 - - - +
326A ASP* 1.3 64.2 + - - +
328A LYS* 3.3 33.4 + - - +
335A LYS* 4.8 11.4 + - - -
344A PHE* 3.6 18.1 - - - -
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Residues in contact with ASP 326 (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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267A VAL* 6.0 1.8 - - + -
322A GLU* 2.7 44.0 + - - +
323A ALA* 4.3 3.9 - - - +
325A ASN* 1.3 80.0 - - - +
327A TYR* 1.3 57.8 + - - +
328A LYS* 3.1 13.0 + - - +
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Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A VAL* 3.7 37.9 - - + -
268A ASP* 6.1 0.2 - - - -
271A HIS* 5.6 1.6 - - - -
323A ALA 3.1 17.7 + - - +
324A LEU 4.6 2.7 - - - -
325A ASN 3.6 0.2 - - - -
326A ASP* 1.3 73.8 - - - +
328A LYS* 1.3 58.8 + - - +
329A THR* 3.2 23.6 + - + -
330A MET* 3.2 44.9 + - + +
331A PHE* 3.0 38.5 + + + +
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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