Contacts of the strand formed by residues 356 - 366 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TYR* 2.7 25.2 + - + +
252A PHE* 2.8 29.1 + - - +
253A SER 3.9 8.5 + - - -
254A ALA* 4.3 8.1 - - - +
285A ALA* 3.4 18.6 - - + +
308A GLY* 3.8 15.9 - - - -
309A VAL 3.5 15.0 - - - +
310A ILE* 3.6 27.7 - - - +
311A LYS* 4.6 2.8 - - - +
316A TRP* 4.2 2.7 - - - -
349A TYR* 3.4 3.5 - - - -
350A SER* 2.9 26.1 + - - -
353A PHE 3.1 20.7 + - - +
354A GLY 3.5 13.2 + - - -
355A ASN* 1.3 82.4 + - - +
357A MET* 1.3 62.5 + - - +
358A ILE* 3.6 6.5 + - + +
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Residues in contact with MET 357 (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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307A GLY 3.5 0.3 - - - +
308A GLY* 3.2 2.9 - - - -
309A VAL* 2.7 61.1 + - + +
315A LEU* 4.2 2.5 - - + +
316A TRP* 3.7 34.5 - - + +
319A GLN* 3.6 30.1 - - + -
348A TYR* 3.2 15.9 - - + +
349A TYR* 3.8 28.7 - - + -
356A ARG* 1.3 72.3 - - - +
358A ILE* 1.3 62.8 + - - +
359A GLN* 3.5 25.4 + - - +
382A ASN* 3.9 10.5 - - - +
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Residues in contact with ILE 358 (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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251A TYR* 3.5 39.3 - - + +
306A TYR* 4.9 3.8 - - + -
307A GLY 3.2 8.3 - - - +
308A GLY* 4.3 1.1 - - - -
348A TYR* 2.9 19.1 + - - +
350A SER* 3.9 26.9 - - - +
353A PHE* 4.2 6.3 - - + -
356A ARG* 4.1 9.2 - - + +
357A MET* 1.3 77.8 - - - +
359A GLN* 1.3 60.2 + - - +
382A ASN* 5.4 0.2 - - - +
387A MET* 3.5 29.5 - - + +
388A GLY 2.9 40.2 + - - +
459A LEU* 5.2 7.0 - - + -
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Residues in contact with GLN 359 (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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284A TRP* 3.5 30.6 - - + -
306A TYR* 3.0 6.9 - - - +
307A GLY 2.8 35.7 + - - +
309A VAL* 3.9 15.9 - - + -
315A LEU* 4.8 1.1 - - + +
319A GLN* 3.0 20.1 + - - -
357A MET* 3.5 16.6 - - - +
358A ILE* 1.3 74.3 - - - +
360A SER* 1.3 87.3 + - - +
379A PRO* 4.2 6.3 - - + -
380A PHE* 3.2 13.5 + - - +
382A ASN* 3.1 32.4 + - - -
388A GLY* 3.4 5.4 - - - +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TRP* 5.1 1.6 - - - -
305A ILE* 3.7 4.5 - - - -
306A TYR* 4.4 0.2 - - - -
359A GLN* 1.3 98.2 + - - +
361A GLY* 1.3 59.2 + - - +
379A PRO* 3.6 3.1 - - - +
380A PHE* 3.0 22.3 + - - +
382A ASN* 5.2 0.2 + - - -
385A VAL* 4.7 4.3 - - - -
386A LEU 4.9 1.5 + - - -
388A GLY* 3.3 3.8 - - - +
389A ALA 3.2 18.2 + - - -
402A TYR* 3.0 26.0 + - - -
404A GLN* 3.0 25.5 + - - -
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Residues in contact with GLY 361 (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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284A TRP* 5.7 0.2 - - - -
304A PRO* 3.8 3.1 - - - +
305A ILE* 3.0 39.8 + - - +
360A SER* 1.3 77.4 - - - +
362A ILE* 1.3 69.3 + - - +
378A LEU 3.4 12.3 - - - -
379A PRO* 4.0 2.2 - - - -
380A PHE* 3.5 14.4 - - - -
402A TYR* 4.6 2.9 - - - -
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Residues in contact with ILE 362 (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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302A LEU* 3.9 28.7 - - + -
303A PHE 3.3 10.3 - - - +
304A PRO* 5.1 0.4 - - + -
305A ILE* 3.6 5.5 - - - +
361A GLY* 1.3 79.5 - - - +
363A LEU* 1.3 73.3 + - - +
364A ALA 4.0 0.6 + - - +
376A LEU 3.7 1.0 - - - +
377A VAL* 3.8 0.9 - - - -
378A LEU* 2.9 43.3 + - + +
380A PHE* 3.8 26.5 - - + -
393A LEU* 3.8 26.0 - - + -
400A VAL* 5.2 1.3 - - + -
402A TYR* 5.4 0.2 - - + -
418A VAL* 4.2 15.0 - - + -
420A ILE* 5.3 1.6 - - + -
430A ILE* 4.0 19.3 - - + -
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Residues in contact with LEU 363 (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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239A TYR* 3.5 42.4 - - + +
261A ILE* 4.5 0.4 - - + -
275A ILE* 4.0 13.9 - - + -
277A PRO* 4.1 7.6 - - + -
287A LEU* 5.9 0.7 - - + -
301A VAL 3.5 1.9 - - - +
302A LEU* 3.2 5.0 - - - -
303A PHE* 2.8 40.4 + - + +
305A ILE* 3.7 20.9 - - + +
362A ILE* 1.3 73.4 - - - +
364A ALA* 1.3 59.7 + - - +
365A CYS* 4.0 15.9 - - - -
375A CYS* 3.9 15.3 - - + -
376A LEU 3.3 19.1 - - - +
377A VAL* 3.8 19.3 - - + -
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Residues in contact with ALA 364 (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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300A TRP* 3.8 18.6 - - + -
301A VAL 3.5 3.8 - - - -
302A LEU* 3.7 21.1 - - + -
362A ILE* 4.0 0.8 + - + -
363A LEU* 1.3 73.2 - - - +
365A CYS* 1.3 60.8 + - - +
375A CYS* 3.1 3.1 - - - -
376A LEU* 2.8 44.8 + - + +
378A LEU* 4.6 9.0 - - + -
427A PRO* 4.1 17.7 - - + -
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Residues in contact with CYS 365 (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 MET* 4.2 16.4 - - + -
261A ILE* 4.0 23.8 - - - -
300A TRP* 3.5 6.3 - - - -
301A VAL* 2.8 44.0 + - - +
303A PHE* 5.1 2.2 - - + -
363A LEU* 4.0 11.7 - - - -
364A ALA* 1.3 72.7 - - - +
366A PRO* 1.3 71.0 - - + +
371A LEU* 4.8 1.1 - - + -
375A CYS* 2.1 44.6 - - - -
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Residues in contact with PRO 366 (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 MET* 4.0 3.1 - - - +
299A GLY 4.4 3.4 - - - +
300A TRP* 3.4 34.9 - - + -
365A CYS* 1.3 86.8 - - + +
367A LEU* 1.3 58.9 + - - +
368A ARG* 3.0 31.7 + - + +
371A LEU* 3.6 18.4 - - + +
374A GLU* 3.5 38.4 - - + +
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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