Contacts of the strand formed by residues 310 - 317 (chain D) in PDB entry 5Y7K
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 ARG 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305D TRP* 3.4 8.3 - - - -
306D ALA* 2.8 35.6 + - + -
307D THR* 3.2 22.9 + - - +
308D GLN 3.7 1.2 - - - -
309D GLU* 1.3 78.8 - - - +
311D ILE* 1.3 62.3 + - - +
327D ILE* 3.7 25.4 - - + -
328D CYS 3.4 3.8 - - - +
329D ASP* 2.7 41.9 + - - +
337D TRP* 4.3 0.2 - - - -
343D ARG* 3.7 11.5 - - - +
367D ASP 4.1 3.9 + - - -
368D GLY 2.4 41.1 + - - -
369D ASN* 2.9 24.7 + - - +
389D ILE* 4.3 9.1 - - - +
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Residues in contact with ILE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ALA* 3.7 6.1 - - + -
268D PHE* 3.6 35.4 - - + -
270D VAL* 4.6 1.3 - - + -
287D ILE* 4.3 10.5 - - + -
303D VAL* 4.1 4.5 - - + -
304D THR 4.0 7.9 - - - +
305D TRP* 3.7 39.9 - - + +
306D ALA* 5.0 0.4 - - - -
310D ARG* 1.3 77.2 - - - +
312D SER* 1.3 71.2 + - - +
313D LEU* 4.0 6.1 - - + -
326D ASP 3.9 0.3 - - - +
327D ILE* 3.7 2.5 - - - +
328D CYS* 2.9 47.8 + - + +
337D TRP* 4.0 18.4 - - + -
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Residues in contact with SER 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D ASP* 4.0 1.4 + - - +
303D VAL* 3.6 1.2 - - - -
304D THR* 2.7 44.4 + - - -
306D ALA 4.8 0.2 - - - +
311D ILE* 1.3 73.2 - - - +
313D LEU* 1.3 74.8 + - - +
314D GLN* 4.8 1.9 - - - +
325D MET* 3.0 29.9 - - - +
326D ASP 3.3 4.5 - - - -
327D ILE* 4.5 2.9 - - - +
362D PRO* 3.9 6.2 - - - +
364D PHE* 3.7 25.4 - - - -
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D PHE* 3.6 50.7 - - + -
287D ILE* 3.9 23.6 - - + -
300D LEU* 4.1 14.6 - - + -
302D ASP 3.7 1.8 - - - -
303D VAL* 4.0 10.5 - - + -
311D ILE* 4.0 11.0 - - + -
312D SER* 1.3 86.9 + - - +
314D GLN* 1.3 60.2 + - - +
315D TRP* 3.9 26.0 - - + +
324D VAL 3.7 1.2 - - - +
326D ASP* 2.5 51.5 + - + +
328D CYS* 5.2 4.5 - - - -
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Residues in contact with GLN 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D LEU* 3.6 7.6 - - - +
301D CYS* 3.1 29.8 + - - -
302D ASP* 3.1 45.1 + - + +
312D SER* 4.8 1.8 - - - +
313D LEU* 1.3 75.5 - - - +
315D TRP* 1.3 60.9 + - - +
323D SER* 5.2 1.8 + - - -
324D VAL 3.4 6.1 - - - +
325D MET* 3.8 20.6 - - + +
359D PRO* 3.2 18.6 - - + +
360D SER 2.8 21.1 + - - -
362D PRO* 3.3 14.5 - - - +
373D LYS* 2.5 28.2 + - - +
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Residues in contact with TRP 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D VAL* 3.7 33.4 - - + -
267D LYS* 5.3 0.2 - - - -
268D PHE* 4.7 11.2 - - + -
287D ILE 4.2 9.2 - - - -
288D THR 4.4 1.6 + - - -
289D ALA* 3.4 30.4 - - + +
290D PRO* 3.6 22.1 - - + +
293D MET* 3.6 21.8 - - + -
298D HIS* 3.5 18.8 - + - -
299D TYR 3.4 20.2 - - - -
300D LEU* 3.8 24.2 - - + -
301D CYS* 4.0 1.6 - - - -
313D LEU* 3.9 36.4 - - + +
314D GLN* 1.3 77.2 - - - +
316D LEU* 1.3 62.2 + - - +
323D SER* 3.1 9.2 - - - -
324D VAL 2.8 35.5 + - - +
326D ASP* 4.7 3.9 + - + +
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D MET* 3.7 4.3 - - - -
298D HIS* 3.1 1.2 - - - -
299D TYR* 2.4 53.6 + - + +
301D CYS* 3.9 17.7 - - + -
315D TRP* 1.3 75.6 - - - +
317D ARG* 1.3 79.8 + - - +
320D GLN* 3.6 50.9 - - + +
322D TYR 3.2 20.4 - - - +
323D SER* 4.2 9.2 - - - -
354D VAL* 4.4 4.9 - - + +
358D ARG* 5.9 1.8 - - - -
359D PRO* 4.6 14.4 - - + -
665D VAL* 6.4 0.2 - - + -
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Residues in contact with ARG 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D SER* 3.1 32.2 + - - +
293D MET* 3.6 17.9 - - - -
295D ILE* 3.7 22.9 - - + +
297D ASP 3.8 8.3 - - - +
298D HIS* 4.1 2.0 - - + +
299D TYR* 3.8 2.0 - - - -
316D LEU* 1.3 92.8 - - - +
318D ARG* 1.3 66.3 + - - +
319D ILE* 3.2 21.2 + - + +
320D GLN* 3.6 5.4 - - - +
321D ASN* 5.7 0.4 - - - -
322D TYR* 3.3 52.5 + - - +
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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