Contacts of the strand formed by residues 545 - 562 (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 ILE 545 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 4.0 0.2 - - - +
31A ARG* 3.0 21.8 + - - +
538A TYR* 2.9 41.1 - - + +
540A PRO* 2.9 29.3 - - + +
543A ARG* 3.0 24.9 + - + +
544A PRO* 1.3 89.3 - - + +
546A VAL* 1.3 68.2 + - - +
547A VAL* 5.5 3.8 - - + -
586A LYS 3.3 6.3 - - - +
587A ALA* 3.7 18.4 - - + -
588A ALA 4.9 3.8 - - - +
589A LEU* 6.1 0.4 - - + -
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.4 29.4 - - + +
30A ALA 6.1 0.7 - - - +
31A ARG* 4.8 7.4 - - + +
43A ILE* 4.1 19.7 - - + -
538A TYR 3.4 3.8 - - - -
539A VAL* 4.0 27.1 - - + -
545A ILE* 1.3 81.7 - - - +
547A VAL* 1.3 71.5 + - - +
548A THR* 6.1 2.2 - - - -
584A GLU 5.4 0.2 - - - -
585A ALA* 3.4 1.1 - - - -
586A LYS* 2.8 49.6 + - + +
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL 4.1 0.5 - - - +
537A LYS* 3.6 1.0 - - - -
538A TYR* 2.7 61.5 + - + +
539A VAL* 5.2 0.2 - - - +
545A ILE* 5.5 3.4 - - + -
546A VAL* 1.3 87.3 - - - +
548A THR* 1.3 69.0 + - - +
583A ILE* 5.5 4.3 - - + -
584A GLU 3.4 9.2 - - - +
585A ALA* 3.9 16.2 - - + -
586A LYS 5.1 0.9 - - - +
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Residues in contact with THR 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 5.3 2.3 + - - -
74A PRO* 5.2 3.6 - - + -
133A ARG* 5.8 3.1 - - - +
504A TYR* 4.6 2.8 + - - -
536A VAL 3.5 5.3 + - - -
537A LYS* 3.7 27.7 - - - +
546A VAL* 6.1 2.7 - - - -
547A VAL* 1.3 82.4 - - - +
549A GLY* 1.3 67.7 + - - +
550A ALA* 5.1 1.0 - - - +
582A GLU 5.2 0.9 - - - +
583A ILE* 3.3 9.3 - - - +
584A GLU* 2.9 56.9 + - + +
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Residues in contact with GLY 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A TYR* 3.9 3.3 + - - -
535A GLY* 3.3 2.3 - - - -
536A VAL* 2.9 34.7 + - - +
548A THR* 1.3 79.6 + - - +
550A ALA* 1.3 65.1 + - - +
582A GLU 3.3 9.4 - - - -
583A ILE* 4.2 5.8 - - - -
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 3.8 10.3 - - - +
93A ARG* 5.2 0.4 - - - +
504A TYR* 3.2 21.1 - - - +
533A GLU* 3.7 16.4 - - - +
534A VAL 3.5 7.4 - - - +
535A GLY* 4.0 1.3 - - - -
548A THR* 5.1 1.6 - - - +
549A GLY* 1.3 77.3 - - - +
551A VAL* 1.3 63.2 + - - +
552A TYR* 5.2 1.3 - - - -
581A VAL* 3.3 8.1 - - - +
582A GLU* 2.8 41.7 + - + +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLU* 3.5 1.5 - - - +
534A VAL* 2.9 53.4 + - + +
535A GLY* 5.1 1.6 - - - -
550A ALA* 1.3 76.7 - - - +
552A TYR* 1.3 68.7 + - - +
580A GLY 3.0 15.9 - - - +
581A VAL* 4.4 14.1 - - + -
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Residues in contact with TYR 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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93A ARG* 3.0 61.3 + - + +
531A GLN* 3.9 11.2 - - - +
532A TYR 3.1 12.3 - - - +
533A GLU* 3.9 7.0 - - + +
550A ALA 5.2 0.9 - - - -
551A VAL* 1.3 85.8 - - - +
553A ASN* 1.3 59.9 + - - +
554A LEU* 3.9 11.0 - - + -
578A ALA* 3.3 25.2 - - + +
579A ARG* 3.2 6.2 - - - +
580A GLY* 3.0 50.2 + - - -
581A VAL 4.1 0.7 - - - -
582A GLU* 3.7 15.7 + - + -
600A THR* 5.7 1.6 - - + +
601A TYR 4.6 0.6 + - - -
602A THR* 3.5 27.0 + - - +
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Residues in contact with ASN 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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530A LYS 3.6 1.7 - - - +
531A GLN* 3.1 4.2 - - - -
532A TYR* 2.7 57.0 + - + +
552A TYR* 1.3 74.1 - - - +
554A LEU* 1.3 60.1 + - - +
555A THR* 4.1 13.3 + - - -
577A ARG* 3.7 29.9 + - - +
578A ALA 3.7 0.7 - - - -
579A ARG* 3.8 17.2 - - - +
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Residues in contact with LEU 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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93A ARG* 4.1 18.4 - - + +
95A PHE* 3.6 29.3 - - + -
134A GLY* 4.8 0.4 - - - -
135A PRO* 3.8 17.7 - - + -
145A PRO* 4.3 11.0 - - + -
146A GLY* 3.8 20.4 - - - +
530A LYS 3.3 5.6 - - - +
531A GLN* 3.5 30.3 - - + +
552A TYR* 3.9 10.1 - - + -
553A ASN* 1.3 74.6 - - - +
555A THR* 1.3 68.4 + - - +
576A ILE 4.0 0.5 - - - +
577A ARG* 3.5 1.7 - - - +
578A ALA* 2.7 44.9 + - + +
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Residues in contact with THR 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO* 5.7 0.2 - - - -
528A LYS 3.4 3.5 - - - +
529A GLY* 3.4 1.3 - - - -
530A LYS* 2.5 52.5 + - + +
553A ASN* 4.1 11.3 + - - -
554A LEU* 1.3 80.7 + - - +
556A LYS* 1.3 62.9 - - - +
557A THR* 3.5 25.3 + - + -
575A GLU* 4.1 14.9 + - + +
576A ILE 3.6 3.8 - - - +
577A ARG* 4.0 15.1 - - - +
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Residues in contact with LYS 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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95A PHE* 3.7 37.0 - - + -
96A ALA 5.2 6.5 + - - -
98A GLU* 6.3 1.4 - - - +
145A PRO* 4.2 16.4 - - + -
512A GLU* 4.9 8.9 + - - -
527A SER* 3.6 27.6 - - - +
528A LYS 3.0 10.5 - - - +
529A GLY* 4.8 0.9 - - - -
554A LEU 4.3 0.2 + - - -
555A THR* 1.3 73.7 - - - +
557A THR* 1.3 65.3 + - - +
559A ASN* 2.9 33.2 + - - +
575A GLU* 3.4 5.4 - - - +
576A ILE* 2.9 35.4 + - + +
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Residues in contact with THR 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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527A SER* 3.2 3.8 - - - -
528A LYS* 2.9 44.7 + - - +
530A LYS* 5.2 8.1 - - + +
555A THR* 3.5 24.0 - - + +
556A LYS* 1.3 79.2 - - - +
558A ASN* 1.3 76.6 + - - +
559A ASN 3.3 1.3 - - - -
574A GLY 3.8 2.9 - - - -
575A GLU* 3.6 20.6 - - - +
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Residues in contact with ASN 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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525A ALA* 3.4 21.4 + - - +
526A PRO 2.6 27.3 + - - +
527A SER* 3.5 11.5 - - - -
528A LYS* 4.8 2.0 - - + +
557A THR* 1.3 82.9 - - - +
559A ASN* 1.3 67.0 + - - +
560A LEU* 3.4 7.0 + - - +
572A GLU* 3.1 28.5 + - - +
573A GLY* 2.9 29.3 + - - +
574A GLY 2.8 9.7 + - - -
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Residues in contact with ASN 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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527A SER* 4.9 0.2 - - - -
556A LYS* 2.9 36.6 + - + +
557A THR 3.3 1.0 - - - -
558A ASN* 1.3 78.5 - - - +
560A LEU* 1.3 78.3 + - - +
561A MET 3.3 0.9 + - - -
572A GLU 3.9 2.8 - - - -
574A GLY* 2.7 40.5 + - - +
575A GLU* 4.1 5.8 - - - +
576A ILE* 3.1 31.2 - - + +
606A TYR* 4.2 10.9 - - - -
608A THR 5.9 0.2 + - - -
609A ASP* 4.7 5.1 + - - -
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Residues in contact with LEU 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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514A SER* 3.7 9.9 - - - +
516A GLN* 3.5 20.6 - - + -
524A PHE* 3.2 62.6 - - + -
525A ALA 5.6 1.3 - - - +
558A ASN* 3.4 5.6 + - - +
559A ASN* 1.3 88.6 + - - +
561A MET* 1.3 58.3 + - - +
570A SER* 4.2 12.6 - - - +
571A VAL 3.5 5.2 - - - +
572A GLU* 3.7 17.3 - - + -
609A ASP* 4.8 1.0 - - - +
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Residues in contact with MET 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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559A ASN 3.3 2.2 + - - +
560A LEU* 1.3 74.1 - - - +
562A ALA* 1.3 60.9 + - - +
564A PRO* 5.3 4.0 - - + -
570A SER* 3.1 11.9 + - - -
571A VAL* 2.7 45.7 + - + +
572A GLU 3.2 21.1 - - - +
573A GLY* 4.2 4.7 - - - +
574A GLY* 3.7 17.0 - - - +
608A THR* 4.1 8.5 - - + +
609A ASP* 3.3 32.3 - - - +
610A THR* 3.1 37.9 - - - +
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Residues in contact with ALA 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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561A MET* 1.3 82.2 - - - +
563A ASP* 1.3 66.3 + - - +
564A PRO* 3.0 4.0 - - - +
569A PHE 4.8 1.8 - - - -
570A SER* 4.8 0.7 - - - +
571A VAL* 4.5 0.7 - - - -
609A ASP* 5.0 1.2 + - - -
610A THR* 2.3 36.4 + - + -
611A THR* 3.4 25.8 - - - +
612A TYR* 6.4 0.7 - - + -
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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