Contacts of the helix formed by residues 529 - 548 (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 SER 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A GLN 3.9 1.4 + - - -
528A PHE* 1.3 78.1 - - - +
530A GLU* 1.3 75.1 + - - +
531A LEU* 3.7 5.9 + - - +
532A GLU* 3.2 38.2 + - - +
533A GLY* 3.2 17.3 + - - -
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Residues in contact with GLU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A SER* 1.3 85.7 - - - +
531A LEU* 1.3 63.2 + - + +
533A GLY* 3.6 1.1 + - - -
534A GLN* 2.9 43.6 + - - +
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Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A GLN* 3.3 45.3 - - + +
475A THR* 4.3 11.7 - - + -
476A ASP* 5.9 0.7 - - + +
479A ILE* 5.0 11.0 - - + -
529A SER* 3.2 6.6 + - - +
530A GLU* 1.3 81.4 + - + +
532A GLU* 1.3 62.7 + - + +
533A GLY 3.1 1.3 - - - -
534A GLN* 2.9 16.4 + - - +
535A VAL* 2.8 47.7 + - + +
684A VAL* 4.5 6.1 - - + -
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Residues in contact with GLU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ILE* 4.7 10.8 - - + -
482A ARG* 2.8 37.8 + - - +
483A MET* 3.5 35.3 - - + +
527A GLN 4.2 2.9 - - - +
528A PHE* 3.3 29.0 - - + -
529A SER* 3.2 33.9 + - - +
531A LEU* 1.3 77.6 - - - +
533A GLY* 1.3 56.2 + - - +
535A VAL* 3.5 2.6 + - - +
536A LEU* 3.0 24.4 + - - +
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Residues in contact with GLY 533 (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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517A TYR* 5.4 5.8 - - - -
528A PHE* 4.4 8.6 - - - +
529A SER 3.2 14.5 + - - -
530A GLU* 3.9 3.8 - - - -
531A LEU 3.1 0.8 - - - -
532A GLU* 1.3 73.3 - - - +
534A GLN* 1.3 57.7 + - - +
536A LEU* 3.2 9.9 + - - +
537A GLN* 3.0 34.7 + - - +
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Residues in contact with GLN 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLU* 2.9 39.9 + - - +
531A LEU* 2.9 18.4 + - - +
533A GLY* 1.3 75.1 - - - +
535A VAL* 1.3 61.9 + - - +
537A GLN* 3.2 10.8 + - - +
538A PHE 3.2 16.6 + - - -
684A VAL* 3.4 20.0 + - + +
685A PRO* 3.4 23.6 + - - +
686A PRO* 2.8 33.4 + - - +
687A SER* 5.5 1.6 - - - -
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Residues in contact with VAL 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LEU* 4.1 19.1 - - + -
475A THR* 4.2 24.0 - - + +
479A ILE* 4.7 3.4 - - + +
480A ASP* 4.5 9.0 - - - -
483A MET* 3.7 26.5 - - + -
531A LEU* 2.8 33.9 + - + +
532A GLU* 3.8 5.2 - - - +
534A GLN* 1.3 68.7 - - - +
536A LEU* 1.3 67.3 + - - +
538A PHE* 3.4 14.7 + - - +
539A HIS* 3.4 20.5 + - + +
684A VAL* 4.4 14.1 - - + -
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Residues in contact with LEU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A MET* 4.4 15.4 - - - +
486A HIS* 4.7 9.0 - - - +
487A PHE* 3.9 39.5 - - + +
490A LEU* 4.6 12.6 - - + -
513A ILE* 6.1 0.7 - - + -
517A TYR* 3.9 34.8 - - + -
528A PHE* 5.5 2.0 - - + -
532A GLU 3.0 14.2 + - - +
533A GLY* 3.4 12.8 - - - +
535A VAL* 1.3 76.9 - - - +
537A GLN* 1.3 66.4 + - - +
539A HIS* 2.9 23.8 + - + +
540A LEU* 3.1 19.6 + - + +
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Residues in contact with GLN 537 (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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533A GLY 3.0 20.9 + - - +
534A GLN* 3.2 11.8 + - - +
536A LEU* 1.3 84.3 - - - +
538A PHE* 1.3 62.2 + - - +
540A LEU* 3.3 21.7 + - - +
541A SER 3.0 18.9 + - - -
685A PRO* 3.9 10.8 - - + -
687A SER 5.4 0.7 - - - +
688A ALA* 3.5 32.3 - - + +
691A ARG* 3.1 47.3 + - + +
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Residues in contact with PHE 538 (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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465A CYS* 5.3 2.9 - - - -
467A LEU* 3.8 35.9 - - + -
534A GLN 3.2 6.7 + - - +
535A VAL* 3.4 12.3 - - - +
537A GLN* 1.3 77.6 - - - +
539A HIS* 1.3 73.0 + + - +
541A SER* 2.6 23.2 + - - -
542A ASN* 3.2 29.4 + - - +
682A GLY* 4.2 2.2 - - - -
683A HIS 3.5 25.8 - - - -
684A VAL* 4.9 2.5 - - + -
685A PRO* 3.8 17.2 - - + +
695A ALA* 3.1 34.8 - - + -
696A VAL* 3.8 18.6 - - + -
7E ALA* 6.2 0.2 - - + -
8E ARG* 4.5 11.4 - - + -
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Residues in contact with HIS 539 (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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467A LEU* 5.0 0.4 - - + +
480A ASP* 3.4 23.1 + - - -
483A MET* 4.0 17.7 - - + -
484A ASP* 2.7 36.9 + - - -
487A PHE* 3.7 39.9 - + + -
535A VAL* 3.4 26.4 + - + +
536A LEU* 2.9 9.2 + - - +
538A PHE* 1.3 92.6 - + - +
540A LEU* 1.3 63.4 + - - +
542A ASN* 3.3 20.4 + - - +
543A LEU 3.4 4.2 + - - -
8E ARG* 4.3 21.9 + - + -
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Residues in contact with LEU 540 (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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487A PHE* 3.6 26.2 - - + -
513A ILE* 4.0 26.9 - - + -
536A LEU* 3.1 23.0 + - + +
537A GLN* 3.3 24.0 + - - +
539A HIS* 1.3 75.8 - - - +
541A SER* 1.3 55.2 + - - +
543A LEU* 2.9 21.4 + - - +
544A GLU* 2.9 17.1 + - - +
551A LEU* 3.8 22.5 - - + +
691A ARG* 3.4 28.0 - - - +
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Residues in contact with SER 541 (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 GLN 3.0 13.1 + - - -
538A PHE* 2.6 22.1 + - - -
540A LEU* 1.3 76.0 - - - +
542A ASN* 1.3 56.5 + - - +
544A GLU* 3.3 14.6 + - - +
545A TYR* 2.8 29.3 + - - +
691A ARG* 3.4 31.4 + - - +
692A GLY* 4.4 5.2 - - - -
695A ALA* 3.7 21.2 - - - +
714A ALA* 4.8 3.1 - - - +
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Residues in contact with ASN 542 (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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487A PHE* 6.1 0.2 - - + -
538A PHE* 3.2 31.3 + - - +
539A HIS* 3.3 15.2 + - - +
541A SER* 1.3 80.7 + - - +
543A LEU* 1.3 59.8 + - - +
545A TYR* 3.5 13.4 - - - +
546A ALA* 3.0 23.7 + - - +
695A ALA* 5.3 2.1 - - - +
696A VAL* 4.4 15.1 - - - +
5E GLN* 3.4 25.6 + - - +
7E ALA* 3.4 25.0 + - - +
8E ARG* 3.7 13.7 + - - +
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Residues in contact with LEU 543 (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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487A PHE* 3.8 28.3 - - + -
491A LEU* 4.0 15.3 - - + -
509A LEU* 3.9 26.0 - - + -
513A ILE* 4.5 1.1 - - + -
539A HIS 3.4 2.7 + - - +
540A LEU 2.9 12.4 + - - +
542A ASN* 1.3 75.2 - - - +
544A GLU* 1.3 61.3 + - - +
546A ALA* 3.2 3.6 + - + +
547A CYS* 2.8 39.7 + - - -
551A LEU* 4.0 16.6 - - + -
559A TRP* 3.5 32.8 - - + -
2E ARG* 4.7 3.6 - - + -
5E GLN* 3.7 12.5 - - - +
10E SER* 4.5 4.9 - - - +
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Residues in contact with GLU 544 (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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540A LEU 2.9 15.9 + - - +
541A SER* 3.5 14.8 - - - +
543A LEU* 1.3 73.7 - - - +
545A TYR* 1.3 55.5 + - - +
547A CYS* 4.5 0.4 - - - +
548A GLY* 2.6 32.7 + - - -
549A SER 3.1 28.1 + - - +
550A ASN* 3.7 9.5 - - - -
551A LEU* 3.5 32.4 + - + +
691A ARG* 2.6 46.7 + - - +
692A GLY* 4.9 2.8 + - - -
714A ALA* 4.6 4.4 - - + +
715A GLY* 4.0 18.9 + - - +
716A GLU 4.8 1.7 + - - -
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Residues in contact with TYR 545 (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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438A ILE* 5.6 6.1 - - - +
541A SER 2.8 16.7 + - - +
542A ASN* 3.5 16.8 - - - +
543A LEU 3.3 0.2 - - - -
544A GLU* 1.3 76.5 - - - +
546A ALA* 1.3 65.6 + - + +
548A GLY* 3.4 6.9 + - - -
659A ILE* 3.7 20.4 - - + +
661A LYS* 5.8 2.9 - - - -
698A TYR* 4.1 19.7 + - - -
712A VAL* 3.6 43.7 - - + +
714A ALA* 3.9 14.0 - - + +
767A TYR* 2.8 31.5 + - - -
904A FAD 5.2 8.7 + - - -
4E MET* 3.8 29.4 + - + +
5E GLN* 4.9 5.4 - - + -
6E THR* 5.3 4.5 + - - -
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Residues in contact with ALA 546 (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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542A ASN 3.0 18.1 + - - +
543A LEU* 3.5 10.1 - - + +
545A TYR* 1.3 79.3 - - - +
547A CYS* 1.3 58.8 + - - +
767A TYR* 3.7 2.8 - - - -
803A GLN* 3.2 26.7 + - - +
1E ALA 3.3 17.6 - - - +
2E ARG* 4.1 7.6 - - - -
4E MET* 3.7 14.8 - - + +
5E GLN* 3.8 20.0 - - + -
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Residues in contact with CYS 547 (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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543A LEU* 2.8 27.6 + - - +
544A GLU* 4.1 1.8 - - - +
546A ALA* 1.3 76.1 - - - +
548A GLY* 1.3 62.7 + - - +
549A SER 4.2 3.6 - - - +
551A LEU* 4.5 6.7 - - - -
554A VAL* 3.8 41.3 - - + -
559A TRP* 4.5 16.4 - - - -
657A GLY* 4.4 0.5 - - - -
767A TYR* 4.1 5.1 - - - -
768A SER 4.2 0.2 - - - +
769A PHE* 3.4 27.7 - - + +
803A GLN* 3.8 9.5 + - - +
1E ALA 4.3 14.6 - - - +
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Residues in contact with GLY 548 (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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544A GLU 2.6 17.4 + - - -
545A TYR 3.4 2.4 + - - -
546A ALA 3.4 2.8 - - - -
547A CYS* 1.3 73.6 - - - +
549A SER* 1.3 57.8 + - - -
657A GLY* 3.0 9.0 - - - -
658A ILE* 2.7 46.4 + - - +
659A ILE* 4.4 2.2 - - - -
715A GLY 5.5 0.7 - - - -
767A TYR* 3.8 16.8 - - - -
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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
------------------------------------------------------------
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