Contacts of the strand formed by residues 313 - 323 (chain D) in PDB entry 5MKF
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 ASN 313 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A THR 3.9 3.4 + - - +
249D TYR* 3.1 35.0 + - - +
252D MET* 3.5 22.8 - - - +
253D MET* 5.0 3.8 - - - -
308D PHE* 2.9 29.9 - - - +
309D ILE* 3.6 26.9 - - + +
310D PHE* 3.4 3.0 + - + -
311D TYR 3.3 2.0 + - - -
312D GLU* 1.3 78.7 - - - +
314D LEU* 1.3 61.3 + - - +
428D VAL* 5.4 4.0 - - + +
429D TYR 3.7 3.8 - - - +
430D ASN* 2.8 33.4 - - - +
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Residues in contact with LEU 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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337A LEU* 6.0 5.4 - - + -
340A GLU* 5.8 6.7 - - + -
341A ILE* 5.4 21.1 - - + -
305D ASN* 3.3 27.6 - - - +
308D PHE* 3.8 14.1 - - + -
309D ILE* 5.6 0.7 - - - -
312D GLU 4.4 0.2 + - - -
313D ASN* 1.3 72.5 - - - +
315D LEU* 1.3 79.5 + - - +
316D LEU* 4.5 7.9 - - + +
428D VAL* 3.2 7.9 - - - +
429D TYR* 2.7 70.8 + - + +
430D ASN* 4.7 0.6 - - - +
431D ALA* 4.9 7.5 - - + +
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Residues in contact with LEU 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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291D LEU* 4.5 23.8 - - + +
292D TYR* 3.9 31.0 - - + +
305D ASN* 4.7 1.4 + - - -
307D SER* 4.4 10.0 - - - +
308D PHE* 3.3 25.6 - - + +
309D ILE* 4.8 3.1 - - + +
314D LEU* 1.3 90.8 - - - +
316D LEU* 1.3 75.0 + - - +
317D GLY 4.6 8.3 - - - +
318D VAL* 5.5 0.7 - - - +
319D PRO* 5.5 2.5 - - + -
397D ARG* 4.2 15.0 + - + +
426D PHE* 4.8 11.2 - - + -
427D SER 3.2 18.8 - - - +
428D VAL* 3.6 14.4 - - + -
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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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314D LEU* 4.8 7.9 - - + -
315D LEU* 1.3 80.0 - - - +
317D GLY* 1.3 75.0 + - - +
318D VAL 3.4 1.6 + - - -
397D ARG* 4.5 3.4 - - - +
427D SER* 3.2 38.2 + - - +
428D VAL* 4.0 1.3 - - - -
429D TYR* 3.6 25.8 - - + +
436D PHE* 3.3 41.1 - - + -
540D GLU* 5.0 9.0 - - + +
541D ASP* 5.9 3.1 - - - +
545D PHE* 5.5 2.3 - - + -
546D PRO* 4.8 15.9 - - + -
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Residues in contact with GLY 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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315D LEU* 4.6 4.3 - - - +
316D LEU* 1.3 83.1 - - - +
318D VAL* 1.3 73.4 + - - +
397D ARG* 3.3 29.9 + - - +
540D GLU 5.0 2.6 + - - -
541D ASP 5.3 1.4 + - - -
542D GLN 4.6 2.2 + - - -
544D THR 4.0 18.8 - - - -
545D PHE* 4.3 6.5 - - - -
546D PRO* 4.5 3.8 - - - -
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Residues in contact with VAL 318 (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 TYR* 3.9 2.9 - - - +
315D LEU* 5.6 1.8 - - - -
316D LEU 3.4 4.1 + - - -
317D GLY* 1.3 82.6 - - - +
319D PRO* 1.3 72.1 - - + +
394D ASP* 5.0 5.4 - - + -
395D LEU 3.1 27.1 - - - +
396D SER 3.7 1.8 - - - +
397D ARG* 3.6 36.1 - - + +
426D PHE* 4.5 4.0 - - - -
427D SER 6.0 0.2 - - - +
543D ASN* 3.7 19.3 - - - +
544D THR* 5.0 0.7 - - - -
545D PHE* 3.4 38.6 - - + +
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Residues in contact with PRO 319 (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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291D LEU* 3.9 19.3 - - + -
292D TYR* 3.5 20.2 - - + +
315D LEU* 5.5 2.5 - - + -
318D VAL* 1.3 87.3 - - - +
320D ARG* 1.3 56.3 + - - +
394D ASP* 3.4 2.4 - - - +
395D LEU* 2.4 67.6 + - + -
424D ILE* 4.9 6.7 - - + -
425D ASP 3.0 11.2 - - - +
426D PHE* 3.5 27.4 - - + -
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Residues in contact with ARG 320 (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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319D PRO* 1.3 74.8 - - - +
321D ILE* 1.3 69.6 - - - +
322D ARG* 3.8 9.5 + - + +
374D LEU* 4.7 23.3 - - - +
375D ASN 5.8 2.0 - - - +
392D TYR* 4.5 17.6 - - + -
393D LEU 3.5 5.6 - - - +
394D ASP* 2.7 32.1 + - - +
423D PHE 4.4 0.3 - - - -
424D ILE* 3.6 0.7 - - - -
425D ASP* 2.4 51.4 + - + +
545D PHE* 3.1 52.4 + - + -
546D PRO 4.3 3.0 + - - -
547D ASN* 4.6 14.1 + - - +
1H NAG 5.5 4.6 + - - -
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Residues in contact with ILE 321 (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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283D THR* 6.0 5.4 - - + -
320D ARG* 1.3 72.8 - - - +
322D ARG* 1.3 66.7 + - - +
323D GLN* 5.1 5.3 - - + +
392D TYR* 3.0 7.8 - - - +
393D LEU* 2.8 50.5 + - + +
395D LEU* 3.6 27.8 - - + -
406D VAL* 6.0 4.0 - - + -
409D LEU* 5.3 7.0 - - + -
414D TRP* 4.7 22.9 - - + -
422D THR* 5.1 7.6 - - + -
423D PHE 3.2 11.0 - - - +
424D ILE* 4.2 22.4 - - + -
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Residues in contact with ARG 322 (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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320D ARG* 3.8 10.9 + - + +
321D ILE* 1.3 76.2 - - - +
323D GLN* 1.3 71.4 + - - +
374D LEU* 4.7 10.0 - - - +
376D GLY* 4.5 14.5 - - - -
377D SER 3.8 22.6 + - - -
378D SER* 5.2 0.6 - - - +
379D HIS* 4.9 2.6 - - - +
386D TYR 5.8 1.0 + - - -
387D SER 5.6 0.6 - - - -
388D GLY* 3.1 31.2 + - - +
389D ALA* 3.5 23.3 - - + -
391D TYR 3.7 5.2 - - - +
392D TYR* 4.7 4.0 - - + -
422D THR* 3.4 1.6 - - - -
423D PHE* 2.4 85.3 + - + +
425D ASP* 5.2 6.6 + - - +
440D ARG* 3.7 10.7 - - - +
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Residues in contact with GLN 323 (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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321D ILE* 5.1 5.2 - - + +
322D ARG* 1.3 83.3 - - - +
324D LEU* 1.3 88.8 + - - +
325D ARG* 5.3 7.3 - - - +
365D ALA* 6.0 0.3 - - - +
388D GLY 5.0 0.2 - - - +
389D ALA* 3.8 2.4 - - - -
390D GLY* 2.8 25.1 + - - -
391D TYR* 3.4 24.1 + - + +
414D TRP* 2.2 60.4 + - - +
415D LEU* 3.7 12.0 - - - +
419D THR* 3.9 7.5 + - + +
421D ALA* 3.2 14.4 - - - +
422D THR* 4.7 5.0 - - + +
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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