Contacts of the helix formed by residues 312 - 327 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASP 3.1 9.8 - - - +
311B THR* 1.3 87.6 - - + +
313B LYS* 1.3 61.4 + - - +
314B SER* 4.3 6.3 - - - +
315B GLU* 2.8 59.8 + - + +
316B ARG* 3.3 8.5 + - - +
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Residues in contact with LYS 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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293B MET* 5.4 0.7 - - - +
297B ASN* 3.8 41.0 + - - +
311B THR 3.5 1.6 + - - -
312B PRO* 1.3 71.4 - - - +
314B SER* 1.3 61.9 + - - +
315B GLU 3.5 0.3 + - - -
316B ARG* 3.5 35.0 + - - +
317B TYR* 4.5 3.6 + - - +
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Residues in contact with SER 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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312B PRO* 3.0 5.3 + - - +
313B LYS* 1.3 80.4 - - - +
315B GLU* 1.3 64.7 - - - +
316B ARG 3.5 0.2 - - - -
317B TYR* 4.5 7.1 + - - +
318B GLU* 4.5 7.8 - - - +
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B THR* 4.1 10.0 - - + +
312B PRO* 2.8 43.0 + - + +
314B SER* 1.3 82.1 - - - +
316B ARG* 1.3 64.0 + - - +
317B TYR 3.3 1.8 - - - -
318B GLU* 3.5 27.0 + - - +
319B HIS* 3.1 27.1 + - - +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TRP* 4.1 19.4 - - + -
293B MET* 3.6 14.1 - - + -
297B ASN* 3.0 32.5 + - - +
300B TRP* 3.3 59.9 - - - +
309B ALA 4.3 2.6 + - - -
311B THR* 2.9 30.8 + - + -
312B PRO* 3.3 9.4 - - - +
313B LYS* 3.5 28.2 + - - +
314B SER 3.5 0.8 - - - -
315B GLU* 1.3 78.4 - - - +
317B TYR* 1.3 63.1 + - - +
318B GLU 3.3 0.3 + - - -
319B HIS* 3.3 4.5 + - - +
320B VAL* 3.2 27.3 + - - +
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Residues in contact with TYR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER* 2.8 45.3 + - - -
289B GLU* 3.4 35.0 + - + +
293B MET* 3.7 34.6 - - + -
313B LYS 4.5 4.4 + - - +
314B SER 5.0 6.1 - - - +
315B GLU 3.3 0.8 - - - -
316B ARG* 1.3 78.2 - - - +
318B GLU* 1.3 59.6 + - + +
320B VAL* 4.4 4.5 - - + -
321B LEU* 2.9 58.5 + - + +
342B HIS* 4.9 7.4 - - - +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B SER 4.5 5.2 + - - +
315B GLU* 3.5 32.3 + - - +
317B TYR* 1.3 79.5 - - + +
319B HIS* 1.3 65.4 + - + +
321B LEU* 3.9 5.0 - - - +
322B GLU* 3.0 28.3 + - - +
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Residues in contact with HIS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TRP* 3.4 58.9 + + + +
311B THR* 4.4 4.8 - - + +
315B GLU* 3.1 36.8 + - - +
316B ARG 3.3 3.2 + - - +
318B GLU* 1.3 78.4 + - + +
320B VAL* 1.3 65.8 + - - +
322B GLU* 3.4 17.7 + - - +
323B ALA* 3.1 22.9 + - - +
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Residues in contact with VAL 320 (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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266B TRP* 4.0 25.8 - - + +
269B ILE* 5.1 2.0 - - + -
270B ALA* 4.3 8.9 - - + +
288B SER 5.4 0.7 - - - +
292B LEU* 4.1 26.0 - - + -
293B MET* 3.9 21.1 - - + -
296B ILE* 3.9 19.5 - - + -
316B ARG 3.2 17.7 + - - +
317B TYR* 3.8 8.1 - - + +
319B HIS* 1.3 77.2 - - - +
321B LEU* 1.3 61.9 + - - +
323B ALA* 3.2 8.4 + - - +
324B LEU* 3.0 26.7 + - + +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER* 4.2 13.7 - - - +
317B TYR* 2.9 44.1 + - + +
318B GLU* 3.9 4.7 - - - +
320B VAL* 1.3 77.6 - - - +
322B GLU* 1.3 61.9 + - - +
324B LEU* 3.3 8.9 + - + +
325B ASN* 3.1 43.9 + - - +
342B HIS* 5.4 11.2 - - + -
344B PHE* 4.0 23.6 - - + -
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Residues in contact with GLU 322 (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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114A GLU* 4.9 8.5 - - - +
318B GLU 3.0 19.0 + - - +
319B HIS* 3.6 19.2 + - - +
321B LEU* 1.3 78.5 - - - +
323B ALA* 1.3 56.6 + - - +
325B ASN* 3.4 4.5 + - - +
326B ASP* 2.9 52.6 + - - +
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Residues in contact with ALA 323 (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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266B TRP* 4.2 6.3 - - + +
267B VAL* 3.8 36.8 - - + +
270B ALA* 4.7 4.7 - - + -
319B HIS 3.1 13.2 + - - +
320B VAL 3.2 8.5 + - - +
322B GLU* 1.3 76.0 - - - +
324B LEU* 1.3 64.4 + - - +
326B ASP* 4.6 0.9 - - - -
327B TYR* 3.2 39.2 + - + +
331B PHE* 3.6 3.4 - - - -
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Residues in contact with LEU 324 (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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270B ALA* 4.1 11.2 - - + -
274B LEU* 4.1 13.0 - - + -
288B SER* 3.9 11.9 - - - -
292B LEU* 3.8 21.1 - - + -
320B VAL* 3.0 25.5 + - + +
321B LEU* 3.6 12.3 - - - +
322B GLU 3.3 0.2 - - - -
323B ALA* 1.3 78.2 - - - +
325B ASN* 1.3 60.3 + - - +
327B TYR 4.1 4.3 - - - +
328B LYS* 5.2 1.4 - - - +
331B PHE* 3.7 53.6 - - + +
344B PHE* 3.7 45.3 - - + -
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Residues in contact with ASN 325 (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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112A TYR* 3.5 6.4 + - + +
321B LEU* 3.1 36.9 + - - +
322B GLU* 3.9 4.6 - - - +
324B LEU* 1.3 76.2 - - - +
326B ASP* 1.3 67.9 + - - +
327B TYR 3.5 0.2 - - - -
328B LYS* 3.3 38.6 - - - +
333B SER* 5.9 1.2 - - - -
335B LYS* 5.4 5.1 - - - +
344B PHE* 3.7 21.3 - - - -
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Residues in contact with ASP 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 4.5 10.3 - - - -
116A PRO* 5.9 2.9 - - - +
117A ASN* 3.7 26.6 + - - +
132A LEU* 3.6 36.5 - - + +
133A CYS* 4.8 0.7 - - - -
322B GLU* 2.9 42.6 + - - +
323B ALA* 5.0 0.3 - - - -
325B ASN* 1.3 81.5 - - - +
327B TYR* 1.3 65.4 + - + +
328B LYS* 3.0 12.3 + - - +
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Residues in contact with TYR 327 (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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132A LEU* 3.9 38.4 - - + +
137A HIS* 4.1 22.2 - + - -
267B VAL* 3.6 42.0 - - + +
323B ALA* 3.2 32.5 + - + +
324B LEU 4.4 2.9 - - - -
325B ASN 3.5 0.2 - - - -
326B ASP* 1.3 77.7 - - + +
328B LYS* 1.3 63.2 + - - +
329B THR* 3.2 3.8 - - - +
330B MET* 3.2 15.4 + - + -
331B PHE* 3.1 35.6 + - + +
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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