Contacts of the strand formed by residues 312 - 321 (chain A) in PDB entry 5YL4
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 TYR 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A PHE* 3.7 25.0 - + - -
307A PRO* 3.2 36.2 - - + +
310A GLY 5.7 0.2 - - - -
311A LYS* 1.3 75.1 - - - +
313A MET* 1.3 60.7 + - - +
314A ALA 4.3 6.5 - - - +
315A CYS* 4.9 6.7 - - + -
340A SER 4.7 2.4 + - - -
341A ILE* 3.8 34.0 - - + +
342A GLN 3.0 19.3 + - - -
343A PHE* 3.3 31.8 - + + -
344A VAL* 3.0 25.0 + - - +
377A MET* 4.4 6.5 - - + +
379A SER* 3.6 34.5 - - - -
380A ASN 3.5 3.1 - - - -
381A THR* 4.1 15.5 - - + -
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Residues in contact with MET 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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261A PRO* 3.9 29.7 - - + +
262A TYR* 4.6 12.8 - - - -
265A ILE* 3.7 22.7 - - + -
311A LYS 4.0 0.4 + - - +
312A TYR* 1.3 73.7 - - - +
314A ALA* 1.3 63.5 + - - +
343A PHE* 4.0 6.1 - - - -
344A VAL* 4.1 19.7 - - + -
346A TRP* 4.5 4.9 - - + -
347A CYS* 3.5 24.9 - - - +
380A ASN* 2.9 48.5 + - + +
382A THR* 3.9 27.6 - - + +
435A VAL* 4.1 11.9 - - + -
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Residues in contact with ALA 314 (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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258A ASN 3.0 28.3 - - - +
259A LEU* 3.9 21.1 - - + +
261A PRO* 5.0 1.6 - - + -
312A TYR* 3.6 3.5 - - - -
313A MET* 1.3 83.1 - - + +
315A CYS* 1.3 62.4 + - - +
343A PHE* 4.0 9.8 - - - -
378A LEU 4.5 0.9 - - - -
379A SER* 3.3 3.3 - - - -
380A ASN* 2.8 29.8 + - + +
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Residues in contact with CYS 315 (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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296A PHE* 4.9 0.7 - - - -
312A TYR* 4.9 6.7 - - + -
314A ALA* 1.3 76.8 - - - +
316A CYS* 1.3 68.0 + - - +
343A PHE* 4.3 11.0 - - + -
350A GLY 4.1 9.0 + - - +
351A PHE* 3.4 33.9 - - + -
352A LYS* 3.3 21.3 + - - +
377A MET* 3.4 37.9 - - - -
378A LEU 3.4 4.0 - - - -
379A SER* 3.9 10.8 - - - +
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Residues in contact with CYS 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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248A LEU* 4.8 2.9 - - - -
249A ASN* 4.4 15.5 - - - +
258A ASN* 4.4 18.4 - - - -
259A LEU* 3.9 17.3 - - + -
315A CYS* 1.3 78.2 - - - +
317A LEU* 1.3 64.0 + - - +
318A LEU* 5.0 7.4 - - + -
351A PHE 5.4 0.2 - - - -
352A LYS* 3.3 25.4 - - - +
376A CYS 3.8 0.9 - - - +
377A MET* 3.3 5.1 - - - +
378A LEU* 2.8 55.4 + - + +
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Residues in contact with LEU 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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292A THR* 4.3 10.8 - - + -
295A CYS* 4.3 6.3 - - - -
296A PHE* 5.5 0.7 - - + -
316A CYS* 1.3 72.8 - - - +
318A LEU* 1.3 63.0 + - - +
319A TYR* 3.6 32.5 - - + +
328A VAL* 4.6 1.3 - - + -
332A ILE* 3.9 22.4 - - + -
351A PHE* 3.8 30.7 - - + +
352A LYS 3.0 9.6 + - - +
353A VAL* 3.5 5.3 - - + +
354A GLY 2.9 27.2 + - - +
375A VAL* 4.0 14.6 - - + -
376A CYS 4.0 0.9 - - - -
377A MET* 3.8 32.5 - - + -
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Residues in contact with LEU 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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237A SER* 3.7 28.9 + - - +
238A ILE* 4.3 10.1 - - - +
241A SER* 5.6 9.2 - - - +
248A LEU* 4.0 23.8 - - + -
249A ASN* 4.2 14.8 - - - +
316A CYS* 4.9 6.1 - - + +
317A LEU* 1.3 78.4 - - - +
319A TYR* 1.3 63.7 + - - +
320A ARG* 4.1 2.3 + - + +
354A GLY* 3.4 8.5 - - - +
375A VAL* 3.3 3.0 - - - +
376A CYS* 2.8 49.3 + - + +
378A LEU* 3.9 28.0 - - + -
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Residues in contact with TYR 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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288A VAL* 4.4 5.6 - - + -
291A ILE* 4.4 8.3 - - + -
292A THR* 2.7 40.5 + - - +
317A LEU* 3.6 23.7 - - + +
318A LEU* 1.3 75.4 - - - +
320A ARG* 1.3 64.4 + - - +
321A GLY 4.3 0.2 - - - -
323A VAL* 3.8 30.7 - - + -
328A VAL* 3.4 27.2 - - + +
353A VAL* 3.7 26.0 - - + -
354A GLY 2.8 13.6 + - - +
355A ILE* 3.5 11.6 - - + -
356A ASN* 3.0 26.8 + - - +
374A ALA 3.3 6.3 - - - -
375A VAL* 3.7 24.5 - - + -
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Residues in contact with ARG 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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27A GLU* 3.0 26.6 + - - +
233A GLN* 4.9 1.2 + - - +
236A SER* 2.5 46.1 + - - -
237A SER* 3.6 20.8 + - - +
240A ALA* 4.2 11.5 - - - +
243A ARG* 4.0 0.4 - - - +
244A PHE* 4.1 14.8 - - - -
318A LEU* 4.1 2.9 + - + +
319A TYR* 1.3 77.3 - - - +
321A GLY* 1.3 59.2 + - - +
323A VAL* 4.9 1.3 - - - -
356A ASN* 3.3 17.9 - - + -
358A GLN* 3.8 23.7 + - - +
359A PRO 5.3 1.2 + - - -
360A PRO* 3.6 34.5 - - + +
361A THR* 5.3 0.6 + - - +
373A ARG* 3.3 3.3 - - - +
374A ALA* 2.7 43.0 + - + +
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Residues in contact with GLY 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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319A TYR 4.3 0.2 - - - -
320A ARG* 1.3 74.0 - - - +
322A ASP* 1.3 61.5 + - - -
323A VAL* 2.9 13.7 + - - +
355A ILE* 4.4 1.2 - - - +
356A ASN 3.0 10.3 + - - +
357A TYR* 3.5 35.2 - - - -
358A GLN 3.6 2.6 + - - -
359A PRO* 3.7 11.0 - - - -
372A GLN 3.4 11.7 - - - -
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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