Contacts of the helix formed by residues 549 - 563 (chain A) in PDB entry 6FWF
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 THR 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.6 30.9 + - + +
29A VAL* 4.8 2.0 - - - +
32A LYS* 4.1 31.4 + - - +
204A ARG* 4.1 10.6 + - - +
547A GLY 3.9 2.0 + - - -
548A SER* 1.3 77.1 - - - +
550A SER* 1.3 71.5 + - - +
551A ALA* 3.9 8.9 + - + +
552A SER* 3.3 27.4 + - - +
553A MET* 3.2 20.9 + - - +
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Residues in contact with SER 550 (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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204A ARG* 5.0 2.8 - - - +
207A GLU* 6.0 1.3 - - - -
209A PHE* 5.3 6.5 - - - -
228A GLU* 3.5 37.2 + - - +
232A TRP* 5.3 3.1 + - - -
549A THR* 1.3 78.3 + - - +
551A ALA* 1.3 53.7 + - - -
553A MET* 3.1 18.3 + - - +
554A ALA* 2.8 36.0 + - - +
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Residues in contact with ALA 551 (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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25A MET* 3.8 27.1 - - + -
28A GLU* 4.9 3.8 - - - +
549A THR* 3.4 10.8 + - + +
550A SER* 1.3 79.5 - - - +
552A SER* 1.3 51.4 + - - +
554A ALA* 3.3 6.0 + - - +
555A ILE* 2.8 41.5 + - + +
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Residues in contact with SER 552 (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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25A MET* 3.7 21.1 + - - +
29A VAL* 3.7 12.7 - - - +
540A LEU* 4.4 19.1 - - - +
544A TYR* 4.2 3.6 - - - -
548A SER* 4.0 19.3 - - - -
549A THR* 3.3 23.6 + - - +
550A SER 3.3 0.4 - - - -
551A ALA* 1.3 74.0 - - - +
553A MET* 1.3 57.5 + - - +
555A ILE* 3.9 5.5 - - - +
556A GLY* 2.8 31.4 + - - -
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Residues in contact with MET 553 (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 PHE* 5.1 5.2 - - + -
213A ASN* 3.6 40.8 - - + +
226A THR* 5.2 3.4 - - + -
228A GLU* 4.5 13.9 - - + -
229A ASN* 3.4 31.0 - - - +
232A TRP* 5.6 3.6 - - + -
544A TYR* 3.6 36.5 - - + -
545A PHE* 5.8 0.2 - - - -
548A SER* 4.7 1.5 - - - +
549A THR 3.2 11.5 + - - +
550A SER* 3.1 30.2 + - - +
552A SER* 1.3 75.3 - - - +
554A ALA* 1.3 53.7 + - - +
557A ALA* 2.8 35.7 + - - +
618A PRO* 5.7 3.0 - - + +
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Residues in contact with ALA 554 (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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232A TRP* 3.5 51.4 - - + +
550A SER* 2.8 19.3 + - - +
551A ALA* 3.7 7.9 - - - +
553A MET* 1.3 71.1 - - - +
555A ILE* 1.3 56.7 + - + +
557A ALA* 3.3 1.8 + - - +
558A CYS* 2.8 36.5 + - - +
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Residues in contact with ILE 555 (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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21A ILE* 3.4 34.8 - - + -
25A MET* 4.0 24.9 - - + -
537A PRO 3.8 11.7 - - - +
540A LEU* 4.6 9.4 - - + -
551A ALA* 2.8 24.5 + - + +
552A SER* 3.9 3.8 - - - +
554A ALA* 1.3 70.0 - - + +
556A GLY* 1.3 60.0 + - - +
558A CYS* 3.6 2.6 - - + +
559A PHE* 2.8 63.6 + - + +
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Residues in contact with GLY 556 (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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537A PRO 4.2 12.6 - - - -
538A GLY* 4.0 3.8 - - - -
540A LEU* 4.3 9.2 - - - -
541A HIS 4.5 0.2 - - - -
544A TYR* 3.2 14.8 - - - -
552A SER 2.8 22.8 + - - -
553A MET 3.8 0.9 - - - -
555A ILE* 1.3 73.7 - - - +
557A ALA* 1.3 49.1 + - - +
560A SER* 2.5 41.9 + - - -
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Residues in contact with ALA 557 (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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232A TRP* 4.3 31.4 - - + +
233A SER* 6.0 0.2 - - - -
236A SER* 3.9 5.7 - - - -
544A TYR* 2.9 14.2 + - + +
553A MET 2.8 22.2 + - - +
554A ALA 3.6 4.9 - - - +
556A GLY* 1.3 69.0 - - - +
558A CYS* 1.3 56.0 + - - +
560A SER* 2.8 15.2 + - - -
561A ALA* 2.8 24.1 + - - +
616A ASN* 3.7 6.4 + - - +
618A PRO* 5.4 7.4 - - + -
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Residues in contact with CYS 558 (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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232A TRP* 4.9 7.9 - - + -
236A SER* 5.2 1.6 - - - +
239A LEU* 3.9 31.7 - - + +
554A ALA 2.8 21.3 + - - +
555A ILE* 3.6 5.8 - - + +
557A ALA* 1.3 72.2 - - - +
559A PHE* 1.3 71.9 + - - +
561A ALA* 3.1 9.4 + - - +
562A LEU* 2.8 47.3 + - - +
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Residues in contact with PHE 559 (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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21A ILE* 3.7 31.2 - - + -
533A LEU* 3.4 37.7 - - + -
534A GLY* 3.0 24.3 - - - +
537A PRO* 3.5 15.0 - - + -
538A GLY* 3.5 11.9 - - - +
555A ILE* 2.8 48.9 + - + +
558A CYS* 1.3 85.9 - - - +
560A SER* 1.3 55.6 + - - +
562A LEU* 3.2 25.4 + - + +
563A GLU 2.8 22.9 + - - -
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Residues in contact with SER 560 (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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538A GLY* 3.7 2.9 - - - -
541A HIS* 3.4 24.5 - - - -
556A GLY 2.5 30.3 + - - -
557A ALA* 2.8 13.0 + - - -
559A PHE* 1.3 69.2 - - - +
561A ALA* 1.3 63.1 + - - +
563A GLU* 3.3 25.9 + - - +
564A VAL* 3.8 9.2 - - - +
613A PHE* 4.4 0.2 - - - -
616A ASN* 2.6 33.0 + - - -
1001A HEM 4.0 7.8 - - - +
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Residues in contact with ALA 561 (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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236A SER* 3.5 36.8 - - - +
239A LEU* 5.2 1.8 - - + -
240A LEU* 3.5 16.5 - - + +
557A ALA 2.8 19.1 + - - +
558A CYS* 3.2 10.1 - - - +
560A SER* 1.3 73.0 + - - +
562A LEU* 1.3 58.0 + - + +
564A VAL* 3.1 25.8 + - - +
613A PHE* 3.6 17.5 - - + -
616A ASN* 3.9 0.6 - - - +
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Residues in contact with LEU 562 (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 LEU* 4.6 24.2 - - + +
240A LEU* 5.3 2.7 - - + -
243A GLY* 5.5 6.7 - - - -
530A ILE 5.2 0.7 - - - +
533A LEU* 6.2 2.2 - - + -
534A GLY* 4.5 11.8 - - - -
558A CYS* 2.8 33.6 + - - +
559A PHE* 3.2 34.7 + - + +
561A ALA* 1.3 73.3 - - + +
563A GLU* 1.3 62.0 + - - +
564A VAL 3.2 0.2 - - - -
565A VAL* 3.6 18.2 - - + +
566A PRO* 3.2 18.4 - - - +
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Residues in contact with GLU 563 (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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490A HIS* 3.8 16.9 - - - -
494A GLU* 4.6 2.3 - - - +
531A PHE* 4.3 14.1 - - + -
534A GLY* 3.3 24.7 - - - +
535A GLY* 3.5 14.6 - - - -
538A GLY* 3.3 32.7 - - - -
539A THR 3.6 1.6 + - - -
541A HIS* 3.3 16.5 + - - -
559A PHE 2.8 11.8 + - - +
560A SER* 3.3 12.5 - - - +
561A ALA 3.2 0.6 - - - -
562A LEU* 1.3 73.6 - - - +
564A VAL* 1.3 58.8 + - - +
566A PRO* 3.4 12.4 - - - +
567A LEU* 3.8 21.3 - - - +
1001A HEM 3.9 19.7 - - + +
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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
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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