Contacts of the strand formed by residues 570 - 590 (chain A) in PDB entry 1QFG
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 570 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLN* 6.0 0.2 - - - -
517A VAL 5.5 0.2 + - - -
518A GLY* 4.6 1.4 - - - -
519A LYS* 4.7 2.3 + - - +
524A PHE* 3.5 31.5 - - - -
560A LEU* 4.2 18.4 - - - +
561A MET 3.1 17.0 + - - -
562A ALA* 4.8 0.8 - - - +
569A PHE* 1.3 84.9 - - - +
571A VAL* 1.3 73.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LYS* 6.5 1.3 - - + -
524A PHE* 4.2 4.7 - - - -
560A LEU* 3.5 6.2 - - - -
561A MET* 2.7 48.0 + - + +
563A ASP* 4.1 19.1 - - - +
564A PRO* 4.0 27.8 - - + -
570A SER* 1.3 80.5 - - - +
572A GLU* 1.3 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A PHE* 3.8 14.0 - - + -
525A ALA* 3.5 27.9 + - - +
558A ASN* 3.1 25.5 + - - +
559A ASN 4.1 2.5 - - - +
560A LEU* 3.7 18.4 - - + -
561A MET* 3.2 19.1 - - - +
571A VAL* 1.3 79.1 - - - +
573A GLY* 1.3 68.9 + - - +
574A GLY 3.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A ASN* 2.9 18.9 + - - +
561A MET* 4.2 3.8 - - - -
572A GLU* 1.3 80.2 - - - +
574A GLY* 1.3 66.3 + - - +
575A GLU* 3.8 2.4 + - - +
608A THR* 3.9 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A ASN 2.8 11.8 + - - -
559A ASN* 2.7 44.3 + - - -
561A MET* 3.7 14.3 - - - -
572A GLU 3.1 3.8 + - - -
573A GLY* 1.3 80.0 - - - +
575A GLU* 1.3 59.5 + - - +
608A THR* 3.4 12.8 - - - -
609A ASP* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A THR* 4.1 14.5 + - + +
556A LYS 3.4 13.2 - - - +
557A THR* 3.6 23.2 - - + +
559A ASN* 4.1 2.3 - - - +
573A GLY 4.5 1.9 - - - +
574A GLY* 1.3 74.7 - - - +
576A ILE* 1.3 66.5 + - - +
577A ARG* 6.1 0.6 - - + +
606A TYR* 3.8 0.9 - - - -
607A THR* 2.8 44.6 + - + +
608A THR* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.6 34.6 - - + -
554A LEU 4.0 0.5 - - - +
555A THR* 3.6 3.5 + - - +
556A LYS* 2.9 38.8 + - + +
559A ASN* 3.1 38.3 - - - +
575A GLU* 1.3 76.3 - - - +
577A ARG* 1.3 70.4 + - - +
604A ALA* 5.2 1.8 - - + -
605A GLU 3.4 11.9 - - - +
606A TYR* 3.5 36.8 - - + +
617A PRO* 4.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ASN* 3.7 14.3 + - - +
554A LEU 3.5 6.3 - - - +
555A THR* 4.0 11.9 - - - +
575A GLU* 6.1 0.7 - - + +
576A ILE* 1.3 76.9 - - - +
578A ALA* 1.3 67.5 + - - +
579A ARG* 3.1 56.1 - - + +
603A ASP* 3.7 2.7 + - - +
604A ALA* 3.1 1.9 - - - -
605A GLU* 2.4 78.2 + - + +
607A THR* 4.2 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG 3.7 23.1 - - - +
95A PHE* 3.8 15.7 - - + -
552A TYR* 3.3 16.7 - - + +
554A LEU* 2.7 39.2 + - + +
577A ARG* 1.3 76.8 - - - +
579A ARG* 1.3 60.0 + - - +
602A THR* 4.7 2.9 - - + -
603A ASP 3.3 7.0 - - - +
604A ALA* 4.0 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A TYR* 3.2 11.4 - - - +
553A ASN* 3.8 14.1 - - - +
577A ARG* 3.1 49.0 - - - +
578A ALA* 1.3 75.4 - - - +
580A GLY* 1.3 58.8 + - - +
601A TYR* 4.9 7.8 + - + -
602A THR* 3.9 1.0 - - - -
603A ASP* 2.3 83.4 + - + +
605A GLU* 4.6 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A VAL* 3.0 10.3 - - - +
552A TYR* 3.0 52.6 + - - -
579A ARG* 1.3 75.3 - - - +
581A VAL* 1.3 65.7 + - - +
601A TYR* 3.0 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLY* 6.3 0.2 - - - -
550A ALA 3.3 12.8 - - - +
551A VAL* 4.4 13.5 - - + -
552A TYR* 4.1 0.2 - - - -
580A GLY* 1.3 79.9 - - - +
582A GLU* 1.3 74.7 + - - +
583A ILE* 4.7 10.8 - - + -
599A TYR* 3.7 7.0 - - + +
600A THR* 3.3 3.8 - - - -
601A TYR* 2.7 58.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 3.6 4.9 + - - -
74A PRO* 3.6 15.9 - - + -
75A GLY* 3.6 8.8 - - - +
93A ARG* 2.5 56.3 + - - +
133A ARG* 3.3 25.2 + - - +
548A THR* 4.5 1.7 - - - +
549A GLY* 3.3 2.9 - - - -
550A ALA* 2.8 38.8 + - + +
552A TYR* 3.7 8.1 + - + -
581A VAL* 1.3 81.6 - - - +
583A ILE* 1.3 65.1 + - - +
599A TYR 3.4 3.4 - - - -
600A THR* 3.9 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 4.0 2.4 - - - +
547A VAL* 5.5 4.5 - - + -
548A THR 3.3 12.8 - - - +
549A GLY* 4.3 5.2 - - - -
581A VAL* 4.7 10.3 - - + -
582A GLU* 1.3 79.6 - - - +
584A GLU* 1.3 68.8 - - - +
585A ALA* 5.1 4.9 - - + -
597A GLY 5.5 0.2 - - - +
598A SER* 3.1 10.1 - - - -
599A TYR* 2.8 63.5 + - + +
1101A DDQ 5.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE 4.8 1.9 - - - +
51A SER* 2.6 33.7 + - - -
52A VAL 5.3 2.9 + - - +
72A TYR 4.1 8.6 - - - +
73A THR* 4.3 8.0 + - - -
74A PRO* 3.4 23.3 - - + +
133A ARG* 4.1 0.7 + - - -
546A VAL 5.4 0.2 - - - -
547A VAL* 3.4 3.2 - - - +
548A THR* 2.9 50.3 + - + +
583A ILE* 1.3 74.1 - - - +
585A ALA* 1.3 71.0 + - - +
586A LYS* 3.5 28.2 - - + +
596A VAL* 5.4 0.7 - - - +
597A GLY 3.5 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A VAL 3.4 6.3 - - - -
547A VAL* 3.9 18.4 - - + -
583A ILE* 5.1 6.7 - - + -
584A GLU* 1.3 80.9 - - - +
586A LYS* 1.3 63.9 + - - +
595A VAL* 4.6 2.0 - - - +
596A VAL* 3.1 2.3 - - - -
597A GLY* 2.6 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 4.7 18.4 + - + +
30A ALA* 3.7 24.0 + - - +
52A VAL* 3.5 24.1 + - - +
57A GLU* 4.1 16.9 + - - -
545A ILE* 3.3 1.0 - - - -
546A VAL* 2.8 52.4 + - + +
547A VAL* 5.1 0.4 - - - +
584A GLU* 3.5 24.9 - - + +
585A ALA* 1.3 75.2 - - - +
587A ALA* 1.3 62.7 + - - +
595A VAL* 3.2 7.4 - - - +
596A VAL* 2.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 4.9 4.8 + - - -
544A PRO 3.3 6.5 - - - -
545A ILE* 3.7 23.3 - - + -
547A VAL* 6.3 1.3 - - + -
586A LYS* 1.3 76.3 - - - +
588A ALA* 1.3 66.6 + - - +
589A LEU* 3.6 14.5 + - + +
594A ASN* 3.7 2.2 - - - +
595A VAL* 2.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 5.3 0.2 - - - -
24A PRO* 3.4 18.2 - - + -
27A THR* 4.8 2.0 + - - +
544A PRO* 3.0 37.0 + - + +
545A ILE* 4.9 3.8 - - - +
587A ALA* 1.3 73.4 - - - +
589A LEU* 1.3 67.4 + - - +
590A SER 3.5 8.7 - - - +
591A ALA* 6.1 0.4 - - - -
594A ASN* 3.2 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ILE* 6.1 0.4 - - + -
587A ALA* 3.6 20.1 + - + +
588A ALA* 1.3 81.6 - - - +
590A SER* 1.3 59.8 + - - +
593A VAL* 2.6 40.0 + - + -
595A VAL* 4.5 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ALA* 3.5 8.8 - - - +
589A LEU* 1.3 77.2 + - - +
591A ALA* 1.3 60.1 + - - +
592A SER* 2.9 17.7 + - - -
593A VAL* 3.1 36.6 + - - +
594A ASN* 4.9 1.0 - - - +
631A TYR* 5.2 0.5 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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