Contacts of the helix formed by residues 402 - 416 (chain A) in PDB entry 5FZ9
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 PRO 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A MET* 5.1 4.3 - - + -
400A MET 3.0 11.6 - - - +
401A VAL* 1.3 91.5 - - + +
403A THR* 1.3 65.9 + - - +
404A GLU* 3.2 4.0 - - + +
405A LEU* 3.1 35.2 + - + +
406A VAL* 3.3 11.4 + - - +
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Residues in contact with THR 403 (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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401A VAL 3.7 2.7 + - - +
402A PRO* 1.3 73.0 - - - +
404A GLU* 1.3 66.2 + - - +
406A VAL 3.4 0.7 + - - -
407A GLU* 3.1 26.3 + - - +
516A PRO* 4.7 16.4 - - + -
570A ARG* 5.9 1.1 + - - -
572A ASN* 3.8 23.9 + - + +
592A GLN* 3.4 40.5 + - + +
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Residues in contact with GLU 404 (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 PRO* 4.4 18.0 - - - +
402A PRO* 3.2 4.7 - - + +
403A THR* 1.3 83.2 - - - +
405A LEU* 1.3 57.3 + - - +
407A GLU* 3.9 13.3 - - - +
408A LYS* 3.3 33.5 + - + +
570A ARG* 6.4 0.7 - - - +
572A ASN* 6.0 1.6 - - - +
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Residues in contact with LEU 405 (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 PHE* 4.1 28.0 - - + -
396A MET* 4.5 8.5 - - + -
401A VAL* 4.3 9.0 - - + -
402A PRO* 3.1 28.7 + - + +
404A GLU* 1.3 75.7 - - - +
406A VAL* 1.3 60.1 + - - +
407A GLU 3.2 1.3 - - - -
408A LYS* 3.4 18.6 + - + +
409A GLU* 2.9 31.8 + - + +
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Residues in contact with VAL 406 (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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390A LYS* 4.3 11.7 - - - +
394A PHE* 4.2 10.1 - - + -
401A VAL* 3.6 28.3 - - + +
402A PRO 3.3 5.5 + - - +
403A THR 3.4 0.9 + - - +
405A LEU* 1.3 76.6 - - - +
407A GLU* 1.3 57.7 + - - +
409A GLU* 3.8 4.6 - - - -
410A PHE* 2.9 29.2 + - - +
492A CYS* 4.1 11.2 - - - -
493A PHE* 3.7 21.6 - - + -
590A PHE* 4.0 10.5 - - + -
592A GLN* 3.2 35.9 - - - +
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Residues in contact with GLU 407 (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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26A PHE* 3.4 25.1 - - + -
28A PRO* 4.0 10.9 - - - +
403A THR 3.1 16.7 + - - +
404A GLU* 3.9 15.4 - - - +
405A LEU 3.2 0.2 - - - -
406A VAL* 1.3 74.0 - - - +
408A LYS* 1.3 65.5 + - - +
410A PHE* 3.2 8.5 + - - +
411A TRP* 3.2 24.6 + - + -
520A TYR* 2.6 32.5 + - - +
570A ARG* 3.0 41.8 + - - +
590A PHE* 3.7 16.8 - - + -
592A GLN* 4.9 1.8 - - - +
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Residues in contact with LYS 408 (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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0A MET* 5.2 17.0 - - - +
26A PHE* 4.5 32.5 - - + +
28A PRO* 6.5 0.2 - - + -
404A GLU* 3.3 21.3 + - + +
405A LEU* 3.7 19.3 - - + +
407A GLU* 1.3 78.9 - - - +
409A GLU* 1.3 62.6 + - - +
411A TRP* 3.4 2.8 + - - +
412A ARG* 3.1 22.4 + - - +
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Residues in contact with GLU 409 (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 TYR* 2.5 43.6 + - + +
394A PHE* 4.3 11.0 - - + -
405A LEU* 2.9 21.7 + - + +
406A VAL* 3.8 5.8 - - - +
408A LYS* 1.3 75.2 - - - +
410A PHE* 1.3 66.4 + - - +
412A ARG* 2.9 40.8 + - - -
413A LEU* 2.9 22.9 + - - +
493A PHE* 3.8 11.2 - - + -
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Residues in contact with PHE 410 (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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90A LEU* 4.4 5.6 - - + -
406A VAL 2.9 18.6 + - - +
407A GLU 3.2 5.5 + - - +
409A GLU* 1.3 76.2 - - - +
411A TRP* 1.3 101.8 + + - +
413A LEU* 3.2 11.2 + - + +
414A VAL* 3.1 47.0 + - + +
493A PHE* 3.5 46.0 - + + -
495A SER* 4.0 21.3 - - - -
555A ILE* 4.4 9.9 - - + -
589A GLY 5.5 1.3 - - - -
590A PHE* 3.8 29.2 - + + -
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Residues in contact with TRP 411 (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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26A PHE* 3.5 34.1 - + + -
92A GLU* 4.9 1.1 - - - -
407A GLU* 3.2 24.1 + - - +
408A LYS 3.4 3.6 + - - +
410A PHE* 1.3 94.8 - + + +
412A ARG* 1.3 66.8 + - - +
414A VAL* 3.6 23.5 - - + +
415A SER* 3.4 13.5 + - - -
498A TRP* 5.4 1.1 - + - -
520A TYR* 3.0 40.3 + + - -
555A ILE* 3.7 21.1 - - + -
556A MET 3.4 20.6 - - - -
557A ASN* 3.4 45.6 + - + +
558A PRO* 3.4 16.2 - - + -
588A SER* 5.6 2.7 - - - -
590A PHE* 4.3 0.8 - + - -
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Residues in contact with ARG 412 (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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0A MET* 4.3 26.5 - - + -
393A TYR* 4.0 3.8 + - - -
408A LYS 3.1 15.3 + - - +
409A GLU* 2.9 45.7 + - - +
410A PHE 3.3 0.2 - - - -
411A TRP* 1.3 75.6 - - - +
413A LEU* 1.3 67.4 + - - +
415A SER* 2.9 21.6 + - - +
416A THR* 3.1 31.2 + - - +
419A GLU* 2.8 37.7 + - - +
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Residues in contact with LEU 413 (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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90A LEU* 3.9 37.0 - - + +
393A TYR* 3.3 27.6 - - + +
409A GLU* 2.9 21.8 + - - +
410A PHE* 3.2 10.5 + - + +
412A ARG* 1.3 87.2 - - - +
414A VAL* 1.3 65.3 + - + +
415A SER 3.3 0.3 + - - -
416A THR* 3.6 8.5 + - - +
419A GLU* 4.1 6.7 - - + +
421A VAL* 4.2 18.4 - - + +
493A PHE* 3.8 32.5 - - + -
1766A CL 2.8 23.2 - - - +
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Residues in contact with VAL 414 (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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90A LEU* 3.4 25.1 - - + +
91A ASN* 3.6 4.9 - - - +
92A GLU* 2.8 42.8 + - + +
410A PHE* 3.1 47.0 + - + +
411A TRP* 3.6 35.4 - - + +
413A LEU* 1.3 82.6 - - + +
415A SER* 1.3 62.3 + - - +
555A ILE* 4.4 7.4 - - + -
1766A CL 3.9 3.5 - - - +
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Residues in contact with SER 415 (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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0A MET* 6.2 0.2 - - - +
92A GLU* 3.8 20.2 - - - -
411A TRP 3.4 12.1 + - - -
412A ARG* 2.9 17.7 + - - +
413A LEU 3.2 0.2 - - - -
414A VAL* 1.3 78.9 - - - +
416A THR* 1.3 65.0 + - - +
417A ILE* 3.5 11.2 + - - +
557A ASN* 6.2 0.9 - - - -
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Residues in contact with THR 416 (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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412A ARG* 3.1 31.2 + - - +
413A LEU 3.6 1.5 + - - +
414A VAL 3.5 0.4 - - - -
415A SER* 1.3 77.7 + - - +
417A ILE* 1.3 61.8 + - - +
418A GLU* 3.2 28.5 + - + +
419A GLU* 3.3 30.1 + - + +
1766A CL 2.8 23.6 - - - +
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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