Contacts of the strand formed by residues 356 - 366 (chain D) in PDB entry 4JF7
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 356 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251D TYR* 2.7 26.6 + - + +
252D PHE* 2.8 29.7 + - - +
253D SER 3.7 9.3 + - - -
254D ALA* 4.3 8.3 - - - +
285D ALA* 3.4 18.7 - - + +
308D GLY* 3.9 15.3 - - - -
309D VAL 3.4 16.4 - - - +
310D ILE* 4.0 24.2 - - - +
311D LYS* 4.6 4.2 - - - +
316D TRP* 4.3 0.9 - - - -
349D TYR* 3.6 1.5 - - - -
350D SER 3.0 24.3 + - - -
353D PHE 3.1 20.0 + - - +
354D GLY 3.4 15.1 + - - -
355D ASN* 1.3 80.0 + - - +
357D MET* 1.3 62.4 + - - +
358D ILE* 3.4 9.2 + - + +
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Residues in contact with MET 357 (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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308D GLY* 3.3 2.8 - - - -
309D VAL* 2.8 64.6 + - + +
315D LEU* 4.1 4.9 - - + +
316D TRP* 3.7 28.9 - - + -
319D GLN* 3.5 36.1 - - + +
348D TYR* 3.2 17.0 - - + +
349D TYR* 3.9 24.2 - - + -
356D ARG* 1.3 71.8 - - - +
358D ILE* 1.3 65.0 + - - +
359D GLN* 3.3 21.6 + - - +
382D ASN* 3.7 12.3 - - - +
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Residues in contact with ILE 358 (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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251D TYR* 3.5 38.8 - - + +
306D TYR* 4.9 4.9 - - + -
307D GLY 3.3 7.6 - - - +
348D TYR* 2.9 17.6 + - - +
350D SER* 3.9 25.6 - - - +
353D PHE* 4.2 7.4 - - + -
356D ARG* 3.8 13.2 - - + +
357D MET* 1.3 75.8 - - - +
359D GLN* 1.3 62.3 + - - +
382D ASN* 5.3 0.3 - - - +
387D MET* 3.6 29.3 - - + +
388D GLY 2.9 40.9 + - - +
459D LEU* 5.4 4.5 - - + -
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Residues in contact with GLN 359 (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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284D TRP* 3.5 32.7 - - + -
306D TYR* 2.9 25.5 - - - +
307D GLY 2.8 13.8 + - - -
309D VAL* 3.8 17.7 - - + -
315D LEU* 4.9 0.9 - - + -
319D GLN* 2.9 21.8 + - - -
357D MET* 3.3 18.7 - - + +
358D ILE* 1.3 76.4 - - - +
360D SER* 1.3 86.2 + - - +
379D PRO* 4.3 6.7 - - + -
380D PHE* 3.2 21.8 + - - +
382D ASN* 3.2 18.7 + - - -
388D GLY* 3.5 4.7 - - - +
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Residues in contact with SER 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D TRP* 5.0 0.7 - - - -
305D ILE 3.6 3.8 + - - -
306D TYR* 4.3 0.2 - - - -
359D GLN* 1.3 100.7 + - - +
361D GLY* 1.3 60.4 + - - +
379D PRO* 3.8 0.5 - - - +
380D PHE* 3.2 20.6 + - - -
382D ASN* 5.2 0.2 + - - -
385D VAL* 4.2 6.3 - - - -
386D LEU 5.3 0.6 + - - -
388D GLY* 3.4 4.8 - - - +
389D ALA 3.3 17.2 + - - -
402D TYR* 2.7 24.9 + - - -
404D GLN* 3.3 25.1 + - - -
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Residues in contact with GLY 361 (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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284D TRP* 5.6 0.2 - - - -
304D PRO* 3.8 2.8 - - - +
305D ILE* 3.0 40.1 + - - +
360D SER* 1.3 76.4 - - - +
362D ILE* 1.3 68.3 + - - +
378D LEU 3.2 12.6 - - - -
379D PRO* 4.1 2.2 - - - -
380D PHE* 3.7 14.4 - - - -
402D TYR* 4.7 2.6 - - - -
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Residues in contact with ILE 362 (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 LEU* 4.0 21.8 - - + -
303D PHE 3.4 8.3 - - - +
304D PRO* 5.0 0.7 - - + -
305D ILE* 3.6 5.2 - - - +
361D GLY* 1.3 80.5 - - - +
363D LEU* 1.3 72.2 + - - +
364D ALA 4.1 1.1 + - - +
376D LEU 3.5 2.3 - - - +
377D VAL* 3.6 1.7 - - - -
378D LEU* 2.8 46.8 + - + +
380D PHE* 3.9 23.1 - - + -
393D LEU* 3.7 32.1 - - + -
400D VAL* 5.3 2.5 - - + -
402D TYR* 5.3 0.7 - - + -
418D VAL* 4.2 14.6 - - + -
420D ILE* 5.3 4.9 - - + -
430D ILE* 4.2 18.2 - - + -
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Residues in contact with LEU 363 (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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239D TYR* 3.7 36.3 - - + +
261D ILE* 4.4 0.7 - - + -
275D ILE* 4.1 11.0 - - + -
277D PRO* 3.8 18.4 - - + -
287D LEU* 5.7 0.9 - - + -
301D VAL 3.3 2.4 - - - +
302D LEU* 3.2 4.5 - - - -
303D PHE* 2.8 46.0 + - + +
305D ILE* 3.7 18.5 - - + +
362D ILE* 1.3 74.3 - - - +
364D ALA* 1.3 59.5 + - - +
365D CYS* 3.9 22.2 - - - -
375D CYS* 4.0 7.0 - - + -
376D LEU 3.2 15.3 - - - +
377D VAL* 3.7 20.2 - - + +
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Residues in contact with ALA 364 (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 TRP* 3.6 22.3 - - + -
301D VAL 3.5 4.3 - - - -
302D LEU* 3.8 17.5 - - + -
362D ILE* 4.1 0.4 - - + -
363D LEU* 1.3 73.1 - - - +
365D CYS* 1.3 61.5 + - - +
375D CYS* 3.1 2.8 - - - -
376D LEU* 2.7 43.0 + - + +
378D LEU* 4.3 13.2 - - + -
427D PRO* 4.1 14.4 - - + -
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Residues in contact with CYS 365 (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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237D MET* 4.2 16.2 - - - -
261D ILE* 3.9 16.6 - - - -
300D TRP* 3.3 4.2 - - - -
301D VAL* 2.6 45.8 + - - +
303D PHE* 4.9 1.8 - - + -
363D LEU* 3.9 18.6 - - - -
364D ALA* 1.3 72.3 - - - +
366D PRO* 1.3 71.9 - - + +
371D LEU* 4.6 1.8 - - + -
375D CYS* 2.1 43.7 - - - -
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Residues in contact with PRO 366 (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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237D MET* 4.4 1.0 - - - +
299D GLY 4.1 5.8 - - - +
300D TRP* 3.4 35.2 - - + +
365D CYS* 1.3 90.0 - - + +
367D LEU* 1.3 61.1 + - - +
368D ARG* 3.0 27.3 + - + +
371D LEU* 3.9 15.8 - - + +
374D GLU* 3.5 38.1 - - + +
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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