Contacts of the helix formed by residues 340 - 359 (chain A) in PDB entry 4FWF
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 LEU 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 4.4 2.2 - - - +
88A GLY* 4.2 11.9 - - - +
89A GLU* 2.6 36.4 + - + +
139A TRP* 3.1 49.4 - - + +
192A ARG* 4.0 27.4 - - + +
193A VAL* 5.5 2.0 - - + -
196A VAL* 3.9 19.2 - - + +
201A TRP* 3.7 19.5 - - + +
339A GLY* 1.3 69.1 - - - -
341A VAL* 1.3 59.8 + - - +
342A ARG 3.0 2.7 - - - -
343A ILE* 2.8 37.7 + - + +
344A ARG 3.7 2.4 + - - -
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 4.7 0.8 + - - -
136A LEU* 6.5 0.4 - - + -
201A TRP* 3.8 12.0 - - + -
202A TYR* 4.7 0.9 - - + -
205A LEU* 3.7 32.1 - - + -
209A PRO* 3.6 42.6 - - + -
306A MET* 4.5 8.5 - - - -
337A VAL* 4.4 6.5 - - + -
338A ARG 4.0 18.8 - - - +
339A GLY* 4.7 0.7 - - - -
340A LEU* 1.3 79.6 - - - +
342A ARG* 1.3 64.4 + - - +
344A ARG* 3.1 8.0 + - + +
345A CYS* 2.9 22.7 + - - -
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TRP* 2.9 32.4 + - + +
140A VAL* 4.2 4.9 - - - +
141A GLN 4.8 0.8 - - - +
150A TRP* 3.2 26.1 - - - -
159A LEU* 3.6 17.9 - - - +
164A ALA* 4.0 20.8 - - - +
332A ILE* 3.5 26.1 + - - +
335A ILE* 2.8 31.7 + - + +
336A ILE* 4.8 0.6 - - - +
337A VAL* 3.2 41.7 - - + +
339A GLY 3.5 11.6 + - - +
340A LEU 3.0 1.0 - - - -
341A VAL* 1.3 83.4 - - - +
343A ILE* 1.3 57.4 + - + +
345A CYS* 3.3 4.0 + - - +
346A VAL* 3.0 36.6 + - - +
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TRP* 4.3 17.5 - - + -
150A TRP* 3.5 65.5 - - + +
193A VAL* 4.2 19.5 - - + +
196A VAL* 4.3 12.8 - - + -
340A LEU* 2.8 23.7 + - + +
342A ARG* 1.3 73.6 - - - +
344A ARG* 1.3 66.3 + - - +
346A VAL* 3.2 1.6 + - - +
347A GLN* 3.0 47.5 + - - +
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Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL* 3.6 32.2 + - + +
197A SER* 4.4 9.3 + - - +
198A ASN 4.3 14.9 + - - -
199A HIS* 4.4 9.3 + - - +
201A TRP* 4.1 12.6 - - + -
202A TYR* 3.4 37.7 - - + +
299A GLU* 5.8 4.4 - - - +
300A TYR* 4.8 11.3 + - - -
306A MET* 3.6 15.3 - - + +
340A LEU 3.7 2.6 + - - -
341A VAL* 3.1 14.7 + - + +
343A ILE* 1.3 77.7 - - - +
345A CYS* 1.3 62.1 + - - +
347A GLN* 3.2 12.7 + - - +
348A GLU* 2.9 51.4 + - - +
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Residues in contact with CYS 345 (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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209A PRO* 4.4 8.7 - - - -
211A LEU* 4.8 4.3 - - - -
306A MET* 3.6 29.6 - - - +
310A LEU* 3.7 13.4 - - + +
335A ILE* 3.9 23.3 - - + -
337A VAL* 4.4 10.8 - - - -
341A VAL* 2.9 26.4 + - - -
342A ARG* 3.3 12.6 - - - +
344A ARG* 1.3 76.0 - - - +
346A VAL* 1.3 56.3 + - - +
349A VAL* 2.9 31.9 + - - +
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Residues in contact with VAL 346 (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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141A GLN* 4.5 8.1 - - - +
150A TRP* 3.7 32.5 - - + -
332A ILE* 3.7 36.0 - - + +
335A ILE* 4.2 19.3 - - + -
342A ARG* 3.0 34.5 + - + +
343A ILE 3.8 4.3 - - - +
344A ARG 3.2 0.2 - - - -
345A CYS* 1.3 75.7 - - - +
347A GLN* 1.3 66.3 + - + +
349A VAL* 3.3 18.2 - - - +
350A GLU* 4.0 3.1 + - - +
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Residues in contact with GLN 347 (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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150A TRP* 4.6 7.2 - - - +
193A VAL* 5.3 4.9 + - - +
196A VAL* 4.7 1.6 - - - +
197A SER* 3.8 30.7 + - - +
343A ILE* 3.0 41.4 + - + +
344A ARG* 3.8 14.5 - - - +
346A VAL* 1.3 81.5 - - + +
348A GLU* 1.3 64.2 + - + +
350A GLU* 3.6 16.0 + - - +
351A ARG* 4.2 7.1 - - - +
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Residues in contact with GLU 348 (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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297A PHE* 5.2 0.5 - - - -
300A TYR* 2.5 32.6 + - - +
306A MET* 3.4 23.6 - - + -
310A LEU* 4.5 5.2 - - + -
344A ARG* 2.9 35.4 + - - +
345A CYS 4.0 1.1 - - - +
347A GLN* 1.3 74.4 - - + +
349A VAL* 1.3 66.1 + - - +
350A GLU 3.0 4.5 + - - -
351A ARG* 2.6 59.1 + - - +
352A ILE* 3.2 20.6 + - + +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.8 28.7 - - + -
313A LEU* 5.5 2.2 - - + -
314A ILE* 4.0 23.2 - - + +
328A PRO* 5.0 6.7 - - + -
331A CYS* 4.6 15.5 - - + -
332A ILE* 4.4 14.8 - - + -
335A ILE* 4.0 15.7 - - + -
345A CYS 2.9 15.5 + - - +
346A VAL 3.3 15.9 - - - +
348A GLU* 1.3 77.0 - - - +
350A GLU* 1.3 61.7 + - + +
352A ILE* 3.9 3.8 - - - +
353A LEU* 3.1 30.2 + - + +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PRO* 3.9 25.7 - - + +
346A VAL 4.8 2.2 - - - +
347A GLN* 3.6 12.5 + - - +
348A GLU 3.0 0.8 - - - -
349A VAL* 1.3 81.6 - - + +
351A ARG* 1.3 66.5 + - + +
353A LEU* 3.4 5.6 + - - +
354A TYR* 3.2 58.8 + - + -
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU* 4.5 6.7 + - - -
297A PHE* 3.3 33.3 - - + -
299A GLU* 2.8 29.5 + - - +
300A TYR* 4.4 0.2 + - - -
347A GLN 4.2 8.3 - - - +
348A GLU* 2.6 56.7 + - - +
350A GLU* 1.3 74.0 - - + +
352A ILE* 1.3 65.5 + - - +
354A TYR* 3.4 9.2 + - - +
355A PHE* 3.1 22.2 + - - +
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Residues in contact with ILE 352 (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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297A PHE* 4.1 14.8 - - + -
300A TYR* 5.3 3.8 - - + +
307A TYR* 3.7 47.3 - - + +
310A LEU* 3.9 33.9 - - + -
311A ARG* 4.6 5.2 - - - -
314A ILE* 4.2 10.3 - - + -
348A GLU* 3.2 23.2 + - + +
349A VAL* 3.9 4.5 - - - +
351A ARG* 1.3 75.7 - - + +
353A LEU* 1.3 64.9 + - - +
355A PHE* 3.2 2.8 + - - +
356A MET* 3.0 41.5 + - + +
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Residues in contact with LEU 353 (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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314A ILE* 4.3 14.1 - - + +
326A LEU* 3.7 34.5 - - + +
327A THR 4.2 9.4 - - - -
328A PRO* 4.2 17.7 - - + -
331A CYS* 3.8 29.4 - - - -
349A VAL* 3.1 19.1 + - + +
350A GLU* 3.6 6.1 - - - +
351A ARG 3.3 0.2 - - - -
352A ILE* 1.3 77.6 - - - +
354A TYR* 1.3 71.9 + - + +
356A MET* 3.2 5.8 + - - +
357A THR* 2.9 43.0 + - - +
362A ILE* 4.4 4.8 - - + +
363A ASN* 4.3 2.0 - - - +
375A LEU 5.6 1.1 - - - +
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Residues in contact with TYR 354 (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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328A PRO* 4.4 10.8 - - + +
350A GLU* 3.2 52.6 + - + +
351A ARG* 3.9 7.0 - - - +
352A ILE 3.4 0.4 - - - -
353A LEU* 1.3 92.4 - - + +
355A PHE* 1.3 57.4 + - - +
357A THR* 3.4 1.8 + - - -
358A ARG* 3.0 31.1 + - - +
375A LEU 3.9 17.9 - - - -
376A LEU* 3.7 12.1 - - + +
377A PRO* 3.7 44.9 - - + +
380A TYR* 4.7 13.4 + + - +
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Residues in contact with PHE 355 (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 ASP* 3.8 30.1 - - + -
293A GLU* 3.9 22.0 - - + -
296A GLU* 3.5 31.6 - - + -
297A PHE* 3.7 20.6 - + + -
307A TYR* 3.9 8.1 - - - -
351A ARG 3.1 14.8 + - - +
352A ILE 3.5 6.7 - - - +
354A TYR* 1.3 77.9 - - - +
356A MET* 1.3 66.9 + - + +
358A ARG* 3.4 21.1 + - - +
359A LYS* 3.0 59.2 + - + +
361A LEU* 5.2 5.6 - - + -
380A TYR* 6.1 0.4 - - - -
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Residues in contact with MET 356 (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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293A GLU* 5.8 0.4 - - - +
307A TYR* 4.9 2.7 - - - +
311A ARG* 3.8 25.6 - - + +
314A ILE* 3.7 20.9 - - - -
315A LEU* 3.5 40.4 - - + -
352A ILE* 3.0 30.7 + - + +
353A LEU* 3.2 4.7 + - - +
355A PHE* 1.3 84.9 - - + +
357A THR* 1.3 62.7 + - - +
359A LYS 3.7 0.3 + - - -
360A GLY 3.2 2.4 + - - -
361A LEU* 2.9 52.3 + - + +
362A ILE* 3.3 20.9 + - + -
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Residues in contact with THR 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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353A LEU* 2.9 24.6 + - - +
354A TYR* 3.6 4.9 - - - -
356A MET* 1.3 74.0 - - - +
358A ARG* 1.3 67.9 + - - +
360A GLY* 2.9 15.6 + - - -
362A ILE* 3.4 12.6 - - - +
363A ASN* 3.3 31.0 + - + +
364A THR* 4.8 0.2 - - - +
375A LEU* 3.9 21.1 + - + +
376A LEU* 3.8 18.6 - - + -
400A GLN* 4.2 1.2 + - - -
404A PHE* 3.8 22.6 - - + -
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Residues in contact with ARG 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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296A GLU* 3.9 20.2 + - - -
354A TYR 3.0 18.0 + - - +
355A PHE* 3.8 25.0 + - - +
357A THR* 1.3 76.2 - - - +
359A LYS* 1.3 71.4 + - - +
360A GLY* 3.1 1.6 + - - -
376A LEU* 4.3 7.6 - - + +
380A TYR* 4.1 24.2 + - + -
400A GLN* 4.5 2.1 + - - -
404A PHE* 3.8 17.8 - - + -
813A VAL 4.7 1.0 - - - +
816A ALA* 5.7 0.2 - - - +
817A SER* 2.9 61.6 + - - +
818A LYS* 4.9 0.2 - - - +
820A ALA* 3.9 22.4 - - + -
821A ALA* 3.6 23.7 - - - +
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Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 2.8 31.9 + - + +
355A PHE* 3.0 53.3 + - + +
356A MET 4.0 5.4 - - - +
357A THR 3.2 0.2 - - - -
358A ARG* 1.3 88.8 - - - +
360A GLY* 1.3 58.9 + - - +
361A LEU* 3.4 21.5 + - + +
813A VAL* 3.4 15.4 - - - +
814A ARG* 5.8 0.7 - - - -
817A SER* 3.6 20.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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