Contacts of the strand formed by residues 312 - 321 (chain B) in PDB entry 5WY8
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 GLU 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B ALA* 3.4 29.1 - - + +
270B PHE* 3.7 27.3 - - + -
271B PHE 3.4 8.7 - - - +
272B GLY* 3.9 7.2 - - - -
273B TYR 3.8 18.5 + - - +
308B GLU* 3.0 5.8 - - - -
309B HIS 2.9 34.6 + - - +
310B LEU* 4.9 3.3 - - - +
311B GLY* 1.3 79.2 - - - +
313B GLN* 1.3 59.6 + - - +
314B GLU 4.4 0.2 + - - -
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Residues in contact with GLN 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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269B ALA 4.0 0.2 - - - +
270B PHE* 3.6 4.9 - - - -
271B PHE* 2.8 47.7 + - + +
272B GLY 5.7 1.2 + - - -
277B VAL* 3.9 20.8 + - - +
279B PRO* 4.1 21.0 - - - +
305B ILE* 3.4 28.3 - - + +
307B LYS 3.3 7.4 - - - +
308B GLU* 4.2 17.9 - - + +
311B GLY 4.1 11.5 + - - +
312B GLU* 1.3 75.8 - - - +
314B GLU* 1.3 57.9 + - - +
315B VAL* 3.8 16.8 + - + -
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Residues in contact with GLU 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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245B LEU* 3.8 21.7 - - + +
268B ARG* 2.2 41.3 + - - +
269B ALA 3.5 9.6 - - - +
270B PHE* 4.2 17.5 - - + +
306B LEU* 2.7 35.5 + - + +
307B LYS* 2.8 39.2 + - + +
312B GLU 4.4 0.2 + - - -
313B GLN* 1.3 72.2 - - - +
315B VAL* 1.3 56.1 + - - +
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Residues in contact with VAL 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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267B CYS 3.8 0.2 - - - +
268B ARG* 3.5 3.3 - - - +
269B ALA 2.9 33.3 + - - +
271B PHE* 3.6 31.9 - - + -
279B PRO* 4.2 15.7 - - + -
281B ILE* 4.2 19.1 - - + -
303B ILE* 4.9 4.0 - - + -
304B ARG 3.6 10.5 - - - +
305B ILE* 3.8 22.2 - - + -
306B LEU* 4.1 3.8 - - - +
313B GLN* 3.8 23.1 - - + +
314B GLU* 1.3 80.1 - - - +
316B SER* 1.3 61.6 + - - +
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B THR* 5.4 2.5 - - - -
267B CYS 2.9 17.0 - - - -
268B ARG* 3.9 8.5 - - - -
281B ILE* 4.7 2.9 - - - -
301B SER* 5.0 1.4 - - - -
303B ILE* 3.6 1.7 - - - -
304B ARG* 3.0 33.5 + - - +
306B LEU* 4.0 6.8 - - - +
315B VAL* 1.3 76.9 - - - +
317B ILE* 1.3 60.2 + - - +
318B SER* 5.7 0.4 + - - -
2D NAG 2.6 45.3 + - - +
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Residues in contact with ILE 317 (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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267B CYS* 2.8 34.8 + - + +
281B ILE* 3.7 43.7 - - + +
282B TYR* 4.6 1.8 - - - +
283B TRP* 3.1 17.0 + - + +
300B GLU* 4.1 27.1 - - + +
301B SER* 3.5 22.7 - - - +
302B ASP* 4.2 1.8 - - - +
303B ILE* 3.7 35.7 - - + +
316B SER* 1.3 75.4 - - - +
318B SER* 1.4 55.7 - - - +
334B CYS* 4.8 0.4 - - - -
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Residues in contact with SER 318 (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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264B ASN* 3.4 18.0 + - - -
265B LEU 2.6 14.8 - - - -
266B THR* 3.0 32.6 - - - +
283B TRP* 3.5 4.8 - - - -
300B GLU* 3.4 3.1 - - - -
301B SER* 2.2 51.5 + - - -
316B SER* 5.7 0.5 + - - -
317B ILE* 1.4 71.1 - - - +
319B LEU* 1.3 58.5 + - - +
320B ILE* 4.2 1.9 + - - -
1D NAG 4.4 10.2 + - - -
2D NAG 5.5 1.6 + - - -
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Residues in contact with LEU 319 (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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263B ALA 4.0 0.5 - - - +
264B ASN* 3.7 1.0 - - - -
265B LEU* 2.6 48.7 + - + +
283B TRP* 3.3 24.0 - - + +
290B ILE* 3.5 38.4 - - + -
298B VAL* 4.3 7.4 - - + -
299B TRP 3.4 22.4 - - - +
300B GLU* 4.7 1.3 - - + +
318B SER* 1.3 73.7 - - - +
320B ILE* 1.3 64.8 + - - +
321B VAL* 4.2 6.0 + - + +
332B TYR* 3.2 43.5 - - + -
349B LEU* 6.4 0.2 - - + -
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Residues in contact with ILE 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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262B SER* 3.9 15.0 - - - +
263B ALA 3.4 11.4 - - - +
264B ASN* 3.5 17.0 - - + +
297B ARG 3.3 1.9 - - - +
298B VAL* 3.1 24.8 - - - +
299B TRP* 3.0 56.7 + - + +
301B SER* 4.7 9.6 - - - +
319B LEU* 1.3 78.4 - - - +
321B VAL* 1.3 68.5 + - - +
322B ASP* 4.2 4.0 - - + +
1D NAG 3.5 37.0 - - + +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B SER* 3.2 1.7 + - - -
263B ALA* 2.9 52.0 + - + +
265B LEU* 6.4 1.1 - - + -
297B ARG 3.3 4.9 - - - +
298B VAL* 3.4 26.7 - - + -
319B LEU* 4.2 7.3 + - + -
320B ILE* 1.3 73.3 - - - +
322B ASP* 1.3 64.9 + - - +
323B SER 4.8 3.6 - - - +
324B VAL* 4.3 15.6 - - + +
328B ASP* 4.6 15.9 - - + +
332B TYR* 4.4 16.8 - - + +
349B LEU* 4.6 14.8 - - + -
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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
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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