Contacts of the helix formed by residues 412 - 430 (chain A) in PDB entry 2FBW
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 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASN* 2.9 14.3 + - - +
79A HIS* 2.9 27.0 + - - -
83A THR* 3.1 39.8 + - - +
99A MET* 3.9 12.0 - - + +
404A HIS* 3.7 18.1 + - + +
408A ARG* 4.4 0.2 - - + -
409A LEU* 3.0 30.6 + - - +
410A GLY 3.1 1.8 + - - -
411A ALA* 1.3 77.9 - - - +
413A SER* 1.3 59.9 + - - +
415A LEU* 3.6 7.5 - - - +
416A ASP* 3.0 26.3 + - - +
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 3.7 17.0 + - - -
397A GLU* 5.2 1.4 + - - +
408A ARG* 3.4 40.8 - - - +
411A ALA* 3.3 1.2 - - - +
412A ASN* 1.3 75.8 - - - +
414A LEU* 1.3 64.1 + - - +
415A LEU 3.1 1.6 - - - -
416A ASP* 3.2 9.1 + - - +
417A LEU* 2.9 40.8 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 4.1 15.5 - - + -
60A ALA* 4.1 30.7 - - + -
63A GLY* 3.7 21.8 - - - +
64A ILE* 3.5 22.4 - - + +
153A THR* 4.0 23.8 - - + -
154A GLY* 4.3 4.5 - - - +
157A LEU* 4.0 17.6 - - + +
411A ALA* 4.5 1.6 + - - +
413A SER* 1.3 79.3 + - - +
415A LEU* 1.3 63.3 + - - +
417A LEU* 3.4 30.4 + - + +
418A VAL* 3.5 12.8 + - - +
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.5 23.2 - - + +
65A ASN 3.4 18.4 - - - +
79A HIS* 3.5 24.0 - - + -
99A MET* 3.8 24.2 - - + +
103A ALA* 3.6 31.0 - - + +
106A ALA* 4.5 4.0 - - + -
107A VAL* 5.2 0.2 - - + -
411A ALA 4.0 6.7 + - - +
412A ASN* 3.6 15.6 + - - +
413A SER 3.1 0.2 - - - -
414A LEU* 1.3 76.0 - - - +
416A ASP* 1.3 67.5 + - - +
417A LEU 3.2 0.2 + - - -
418A VAL* 3.2 2.6 + - - +
419A VAL* 3.0 42.8 + - + +
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Residues in contact with ASP 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MET* 3.8 13.9 - - - -
365A TYR* 4.1 6.1 + - - -
396A GLY* 4.1 22.9 + - - +
399A ALA 5.5 1.2 - - - +
401A ALA* 5.9 1.1 - - - +
403A VAL* 3.8 7.7 - - - +
404A HIS* 3.1 26.9 + - - +
412A ASN 3.0 20.1 + - - +
413A SER* 3.3 7.8 + - - +
415A LEU* 1.3 75.1 - - - +
417A LEU* 1.3 64.5 + - - +
420A PHE* 3.0 44.6 + - - +
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 3.6 17.4 - - - +
29A ALA* 3.6 27.2 - - + +
32A ARG* 4.5 0.2 - - - +
57A THR* 3.5 24.9 - - - +
157A LEU* 5.0 1.3 - - + -
396A GLY* 3.6 25.8 - - - +
397A GLU* 4.1 8.5 - - + +
413A SER* 2.9 35.2 + - - +
414A LEU* 3.6 26.7 - - + +
415A LEU 3.1 0.4 - - - -
416A ASP* 1.3 77.6 - - - +
418A VAL* 1.3 61.1 + - + +
421A GLY* 3.0 25.6 + - - -
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Residues in contact with VAL 418 (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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28A GLY 4.7 0.4 - - - +
32A ARG* 3.7 19.0 + - + +
64A ILE* 4.3 11.0 - - + -
106A ALA* 4.0 24.7 - - + +
109A GLU* 5.4 3.7 - - - +
110A LEU* 4.4 22.4 - - + -
157A LEU* 4.7 6.3 - - + -
161A LEU* 4.2 25.1 - - + -
414A LEU 3.5 12.0 + - - +
415A LEU* 3.6 8.3 - - - +
417A LEU* 1.3 80.0 - - + +
419A VAL* 1.3 69.4 + - - +
422A ARG* 3.1 25.5 + - - +
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 3.5 34.2 + - + -
99A MET* 4.1 23.6 - - + +
102A GLN* 4.3 12.3 - - + -
106A ALA* 4.0 15.9 - - + -
415A LEU* 3.0 41.6 + - + +
416A ASP 4.1 1.8 - - - +
418A VAL* 1.3 79.4 - - - +
420A PHE* 1.3 65.5 + - + +
422A ARG* 3.5 5.0 - - - +
423A ALA* 2.9 22.9 + - - +
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Residues in contact with PHE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 3.8 15.7 - - + -
98A TYR* 4.1 12.3 - + - -
99A MET* 3.9 19.3 - - + -
372A THR* 6.0 0.4 - - - -
373A ASN 5.5 0.2 - - - -
374A TYR* 3.5 30.1 - - - -
376A GLY* 5.1 7.9 - - - -
394A ALA 5.4 1.1 - - - +
395A CYS* 3.8 17.0 - - + -
401A ALA* 4.4 13.9 - - + -
403A VAL* 3.6 33.0 - - + -
416A ASP* 3.0 37.0 + - - +
419A VAL* 1.3 75.8 - - + +
421A GLY* 1.3 62.2 + - - +
422A ARG 3.3 0.2 - - - -
423A ALA* 3.6 11.1 - - + +
424A CYS* 2.9 33.9 + - - -
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Residues in contact with GLY 421 (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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29A ALA 4.0 12.3 - - - -
32A ARG* 4.5 0.9 - - - -
33A ALA* 3.5 21.5 - - - +
395A CYS* 3.8 19.0 - - - +
417A LEU 3.0 20.1 + - - -
418A VAL 4.2 0.4 - - - -
420A PHE* 1.3 78.3 - - - +
422A ARG* 1.3 60.5 + - - +
424A CYS* 3.5 0.9 + - - +
425A ALA* 3.3 14.6 + - - +
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Residues in contact with ARG 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.4 41.3 - - - +
39A GLU* 5.3 2.2 + - - +
98A TYR* 4.6 6.6 + - - +
102A GLN* 4.8 9.9 + - - +
106A ALA* 6.6 0.7 - - - +
109A GLU* 3.9 12.4 + - - -
418A VAL 3.1 20.9 + - - +
419A VAL* 3.5 5.6 - - - +
421A GLY* 1.3 76.3 - - - +
423A ALA* 1.3 57.7 + - - +
425A ALA* 3.1 7.1 + - + +
426A LEU* 2.9 65.2 + - + +
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Residues in contact with ALA 423 (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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98A TYR* 4.0 26.2 - - + +
374A TYR 4.7 1.8 - - - +
375A LYS* 3.9 13.5 - - - +
419A VAL 2.9 17.7 + - - +
420A PHE* 3.8 17.7 - - + +
421A GLY 3.3 0.4 - - - -
422A ARG* 1.3 72.5 - - - +
424A CYS* 1.3 66.4 + - - +
426A LEU* 3.7 7.1 - - - +
427A THR* 2.8 30.6 + - - +
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Residues in contact with CYS 424 (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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33A ALA* 4.9 2.2 - - + -
37A LEU* 6.4 0.2 - - + -
210A VAL* 4.3 13.7 - - + -
375A LYS 4.0 5.8 + - - -
376A GLY* 3.9 11.9 - - - -
393A TYR* 3.9 28.3 - - + -
394A ALA 3.7 23.8 - - - -
395A CYS* 3.8 11.7 - - - -
420A PHE* 2.9 25.5 + - - +
421A GLY 3.7 5.2 - - - +
423A ALA* 1.3 75.1 - - - +
425A ALA* 1.3 63.8 + - - +
427A THR* 3.2 1.4 + - - -
428A ILE* 3.0 30.8 + - - +
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Residues in contact with ALA 425 (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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33A ALA* 4.1 5.3 - - - +
36A GLY* 3.8 33.4 - - - +
37A LEU* 3.8 23.7 - - + +
421A GLY 3.3 9.2 + - - +
422A ARG* 3.1 11.5 + - + +
424A CYS* 1.3 80.2 - - - +
426A LEU* 1.3 62.8 + - + +
428A ILE* 3.3 2.1 + - - +
429A ALA* 2.9 25.4 + - - +
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 4.1 15.7 - - - +
422A ARG* 2.9 64.7 + - + +
423A ALA* 3.7 5.2 - - - +
425A ALA* 1.3 76.6 - - + +
427A THR* 1.3 57.5 + - - +
429A ALA* 3.3 8.8 + - + +
430A GLU* 2.9 31.3 + - - +
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Residues in contact with THR 427 (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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375A LYS* 3.0 32.7 + - + +
377A GLN* 3.8 20.6 - - + +
393A TYR* 3.3 26.0 - - + +
423A ALA* 2.8 27.3 + - - +
424A CYS 3.6 3.6 - - - -
426A LEU* 1.3 72.5 - - - +
428A ILE* 1.3 58.0 + - - +
430A GLU* 3.3 6.1 + - - +
431A THR* 2.8 37.8 + - - +
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Residues in contact with ILE 428 (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 ASP 6.1 0.2 - - - +
21A ALA* 5.4 1.3 - - + -
37A LEU* 3.8 25.6 - - + -
42A PHE* 4.1 16.4 - - + -
208A ASN* 3.6 35.2 - - + +
210A VAL* 4.0 20.0 - - + -
393A TYR* 3.4 41.7 - - + +
424A CYS 3.0 17.9 + - - +
425A ALA 3.7 3.4 - - - +
427A THR* 1.3 74.4 - - - +
429A ALA* 1.3 58.1 + - - +
431A THR* 3.0 3.5 + - - -
432A CYS* 2.8 31.2 + - + +
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Residues in contact with ALA 429 (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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40A ALA* 4.1 16.2 - - + -
42A PHE* 3.6 25.6 - - + -
425A ALA 2.9 17.2 + - - +
426A LEU* 3.7 9.2 - - + +
428A ILE* 1.3 77.2 - - - +
430A GLU* 1.3 57.3 + - - +
432A CYS 3.3 12.6 - - - +
433A LYS* 4.0 13.0 + - - -
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Residues in contact with GLU 430 (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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426A LEU 2.9 16.5 + - - +
427A THR* 3.8 6.1 - - - +
428A ILE 3.2 0.2 - - - -
429A ALA* 1.3 75.6 - - - +
431A THR* 1.3 59.7 + - - +
432A CYS 4.9 0.2 - - - -
433A LYS* 5.7 3.1 - - - +
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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