Contacts of the helix formed by residues 384 - 402 (chain a) in PDB entry 5W97
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 GLY 384 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247a ILE* 4.3 0.7 - - - -
344a PHE* 3.0 38.5 - - - -
348a PHE* 4.9 6.7 - - - -
379a TYR 3.0 8.9 + - - -
380a VAL* 3.0 13.9 + - - -
383a MET* 1.3 76.4 - - - +
385a ALA* 1.3 67.2 + - - +
386a VAL 3.3 0.6 + - - -
387a PHE 3.3 1.6 + - - -
388a ALA 3.2 10.2 + - - -
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Residues in contact with ALA 385 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70a VAL* 4.4 13.7 - - + -
74a MET* 3.4 13.6 - - + +
246a LEU 4.1 16.6 - - - +
247a ILE* 3.5 10.2 - - + +
380a VAL 2.9 8.7 + - - -
381a LEU* 3.1 31.1 + - + +
384a GLY* 1.3 73.5 - - - +
386a VAL* 1.3 62.7 + - - +
388a ALA* 3.3 1.0 + - - +
389a ILE* 3.1 26.8 + - - +
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Residues in contact with VAL 386 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69a MET* 4.3 11.9 - - + -
70a VAL* 5.4 0.2 - - + -
381a LEU 3.0 17.9 + - - +
382a SER* 3.3 26.2 - - - +
384a GLY 3.3 0.4 - - - -
385a ALA* 1.3 76.7 - - + +
387a PHE* 1.3 61.7 + - + +
389a ILE* 3.2 11.7 + - + +
390a MET* 2.8 36.9 + - + +
417a MET* 5.2 5.6 - - - -
601a HEA 3.8 57.7 - - + -
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Residues in contact with PHE 387 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254a ILE* 5.2 0.2 - - - +
340a TRP* 3.6 61.6 - + + +
343a GLY* 3.9 3.1 - - - -
344a PHE* 3.8 11.9 - - + -
347a LEU* 3.5 26.7 - - + -
382a SER 3.8 7.9 - - - -
383a MET* 3.3 39.9 - - + +
384a GLY 3.3 3.6 + - - +
386a VAL* 1.3 81.1 - - + +
388a ALA* 1.3 58.1 + - - +
390a MET* 3.7 0.2 - - - +
391a GLY* 2.9 23.2 + - - -
414a PHE* 4.1 17.5 - + - -
417a MET* 4.3 9.6 - - + -
418a PHE* 4.3 14.6 - + - -
421a VAL* 4.2 16.6 - - + -
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Residues in contact with ALA 388 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74a MET* 4.4 1.3 - - + -
250a GLY* 3.8 35.9 - - - +
253a MET* 4.0 12.2 - - + +
254a ILE* 3.9 20.4 - - + -
257a ILE* 4.8 0.3 - - - +
344a PHE* 4.1 3.7 - - + -
384a GLY 3.2 12.7 + - - +
385a ALA 3.7 7.2 - - - +
387a PHE* 1.3 74.3 - - - +
389a ILE* 1.3 57.5 + - - +
391a GLY* 4.5 0.7 - - - +
392a GLY* 2.7 31.4 + - - -
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Residues in contact with ILE 389 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69a MET* 4.2 22.9 - - - -
70a VAL* 4.3 15.3 - - + -
73a ILE* 3.7 28.5 - - + -
74a MET* 3.8 31.0 - - + -
78a PHE* 4.2 4.9 - - + -
253a MET* 4.6 5.6 - - + -
385a ALA 3.1 18.4 + - - +
386a VAL* 3.4 14.4 - - + +
388a ALA* 1.3 73.2 - - - +
390a MET* 1.3 57.1 + - - +
392a GLY* 3.1 1.0 + - - -
393a PHE* 2.6 37.9 + - + +
601a HEA 4.4 26.5 - - + -
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Residues in contact with MET 390 (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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340a TRP* 3.5 42.2 - - + -
386a VAL* 2.8 30.6 + - + +
389a ILE* 1.3 73.3 - - - +
391a GLY* 1.3 58.3 + - - +
393a PHE* 3.3 11.3 + - + +
394a VAL* 2.9 40.1 + - + +
413a HIS* 3.6 24.7 - - + +
417a MET* 5.3 2.7 - - - +
468a MET* 3.9 27.4 - - + -
601a HEA 4.1 32.3 - - + -
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Residues in contact with GLY 391 (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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254a ILE* 6.3 0.7 - - - -
257a ILE* 3.7 9.5 - - - +
337a ALA* 3.6 12.9 - - - +
340a TRP* 3.4 28.0 - - - -
341a ALA 5.2 0.2 - - - -
387a PHE 2.9 13.8 + - - -
388a ALA* 3.9 0.9 - - - -
390a MET* 1.3 74.1 - - - +
392a GLY* 1.3 64.3 + - - +
394a VAL* 3.6 0.4 + - - -
395a HIS* 3.1 25.1 + - - +
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Residues in contact with GLY 392 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78a PHE* 3.8 6.7 - - - -
253a MET* 4.2 8.3 - - - -
257a ILE* 3.7 12.6 - - - +
388a ALA 2.7 21.8 + - - -
389a ILE 3.5 0.7 - - - -
391a GLY* 1.3 72.5 - - - +
393a PHE* 1.3 57.6 + - - +
395a HIS* 3.2 1.1 + - - -
396a TRP* 2.9 49.1 + - - +
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Residues in contact with PHE 393 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20a LEU* 5.5 4.9 - - + -
78a PHE* 3.6 16.4 - + + -
389a ILE* 2.6 22.4 + - + +
390a MET* 3.3 14.6 - - + +
392a GLY* 1.3 71.5 - - - +
394a VAL* 1.3 63.7 + - + +
397a PHE* 2.8 67.9 + + + +
400a PHE* 5.4 8.2 - + - -
405a LEU* 5.2 5.8 - - + -
468a MET* 5.4 2.5 - - + -
472a ILE* 4.0 34.1 - - + -
601a HEA 3.8 39.7 - - + -
101l TGL 4.3 21.5 - - + -
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Residues in contact with VAL 394 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336a PRO* 3.9 33.0 - - + -
337a ALA* 4.0 11.2 - - + +
340a TRP* 4.3 15.3 - - - +
390a MET* 2.9 25.3 + - + +
391a GLY 4.1 3.1 - - - +
393a PHE* 1.3 84.9 - - + +
395a HIS* 1.3 63.6 + - - +
397a PHE* 3.9 1.4 - - - +
398a PRO* 3.6 14.4 - - - +
405a LEU* 3.9 29.0 - - + +
407a ASP* 5.4 2.0 - - - +
410a ALA* 4.8 6.5 - - + -
413a HIS* 5.9 2.2 - - - +
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Residues in contact with HIS 395 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256a HIS* 5.1 1.8 + - - +
257a ILE* 4.2 12.1 - - + +
260a TYR* 3.8 37.3 - + + +
261a TYR* 2.7 35.9 + + + -
337a ALA* 3.7 12.3 - - + +
391a GLY 3.1 19.3 + - - +
392a GLY 3.2 2.2 + - - +
394a VAL* 1.3 79.1 - - - +
396a TRP* 1.3 106.5 + + - +
398a PRO* 3.5 6.6 - - - +
491a ASN* 5.8 1.0 + - - -
493a GLU* 4.8 0.8 + - - -
494a TRP* 3.3 36.3 + + - -
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Residues in contact with TRP 396 (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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78a PHE* 4.2 4.0 - + - -
82a LEU* 3.9 24.7 - - + -
86a MET* 3.9 14.6 - - + -
184a PHE* 5.5 1.3 - + - -
253a MET* 4.0 29.8 - - + -
256a HIS* 3.9 27.6 - + + -
257a ILE* 4.7 2.9 - - + -
392a GLY* 2.9 32.5 + - - +
395a HIS* 1.3 96.3 + + - +
397a PHE* 1.3 57.0 + - - +
398a PRO* 3.2 2.9 - - - -
399a LEU* 2.7 43.0 + - + +
400a PHE* 3.0 32.8 + - + -
493a GLU* 2.7 32.1 + - - +
494a TRP* 3.5 23.0 - + - +
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Residues in contact with PHE 397 (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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393a PHE* 2.8 51.8 + + - +
394a VAL 3.9 4.0 - - - +
396a TRP* 1.3 75.3 - - - +
398a PRO* 1.4 69.6 - - + +
399a LEU 3.1 0.3 + - - -
400a PHE* 3.2 9.5 + + - +
401a SER* 2.9 56.2 + - - -
403a TYR* 3.3 17.3 - - + -
405a LEU* 3.9 24.0 - - + -
472a ILE* 4.2 15.0 - - + -
475a ALA* 4.0 28.5 - - + -
476a PHE* 4.1 13.0 - + - -
101l TGL 4.3 15.3 - - + -
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Residues in contact with PRO 398 (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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394a VAL 3.6 8.1 - - - +
395a HIS 3.5 13.9 - - - +
396a TRP 3.4 4.3 - - - -
397a PHE* 1.4 94.5 - - + +
399a LEU* 1.3 55.3 + - - +
401a SER* 4.1 0.2 - - - +
402a GLY* 2.9 22.7 + - - -
403a TYR 3.4 18.8 - - - +
404a THR* 4.4 13.2 - - + -
405a LEU* 5.2 2.2 - - + +
482a VAL* 3.7 22.4 - - + -
494a TRP* 4.2 10.8 - - + -
498a CYS* 3.1 14.5 - - - +
1m ILE* 4.5 10.8 - - + -
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Residues in contact with LEU 399 (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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81a TRP* 5.0 0.4 - - + -
82a LEU* 4.1 10.8 - - + -
85a LEU* 4.4 8.1 - - + -
396a TRP* 2.7 38.5 + - + +
398a PRO* 1.3 73.3 - - - +
400a PHE* 1.3 69.0 + - + +
493a GLU* 3.3 38.8 - - + +
494a TRP* 3.7 30.7 - - + -
497a GLY 3.6 22.7 - - - +
498a CYS* 4.0 3.4 - - - -
499a PRO* 3.2 24.8 - - - +
500a PRO* 3.7 12.8 - - + +
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Residues in contact with PHE 400 (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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20a LEU* 4.0 22.4 - - + -
78a PHE* 3.7 34.8 - + - -
81a TRP* 3.3 55.5 - + + -
82a LEU* 4.3 11.7 - - + -
393a PHE* 5.4 7.4 - + - -
396a TRP* 3.0 37.0 + + + -
397a PHE* 3.9 8.1 - - - +
399a LEU* 1.3 79.8 - - + +
401a SER* 1.3 57.2 + - - +
499a PRO* 3.2 4.3 - - - +
10l ASN* 3.0 29.3 + - - +
101l TGL 3.5 26.8 - - + +
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Residues in contact with SER 401 (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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397a PHE* 2.9 48.3 + - - -
400a PHE* 1.3 77.2 - - - +
402a GLY* 1.3 59.1 + - - +
403a TYR* 2.8 29.8 + - - +
476a PHE* 4.0 20.0 - - - -
499a PRO* 4.2 4.4 - - - +
7l PRO* 3.8 14.4 - - - +
8l GLY 3.9 4.0 + - - -
10l ASN* 4.5 2.6 - - - +
101l TGL 4.2 9.2 - - - -
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Residues in contact with GLY 402 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398a PRO 2.9 17.4 + - - -
400a PHE 3.7 1.2 - - - -
401a SER* 1.3 77.5 + - - +
403a TYR* 1.3 62.9 + - - +
481a GLU* 3.4 8.3 - - - +
482a VAL* 3.2 24.0 + - - -
498a CYS* 3.5 27.3 - - - +
499a PRO* 3.6 4.1 - - - -
7l PRO* 4.3 5.1 - - - +
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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
------------------------------------------------------------
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