Contacts of the strand formed by residues 502 - 512 (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 THR 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLN* 3.2 40.4 - - - +
494A ASN* 4.2 8.7 - - + -
495A TYR 3.1 21.1 - - - +
496A LEU* 3.2 28.9 - - + +
500A GLY 4.7 1.0 - - - -
501A VAL* 1.3 77.3 + - - +
503A PRO* 1.3 60.6 - - - +
504A TYR* 3.9 2.2 + - - -
536A VAL* 3.2 2.4 - - - -
537A LYS* 2.5 51.9 + - - +
539A VAL* 4.7 1.6 + - - +
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Residues in contact with PRO 503 (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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494A ASN* 3.3 0.5 - - - -
495A TYR* 2.6 63.1 + - + +
497A PHE* 5.1 9.0 - - + -
501A VAL* 3.3 20.4 - - + +
502A THR* 1.3 80.0 - - - +
504A TYR* 1.3 62.0 + - - +
536A VAL* 3.6 21.3 - - + -
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Residues in contact with TYR 504 (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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47A PRO* 3.6 29.8 - - + -
48A GLN 4.3 0.4 - - - -
49A SER* 3.6 5.0 + - - -
493A VAL 3.0 11.4 - - - +
494A ASN* 2.7 33.9 - - - +
502A THR 4.1 2.0 - - - -
503A PRO* 1.3 74.0 - - - +
505A PHE* 1.3 73.8 + - - +
533A GLU* 2.8 37.7 + - + -
534A VAL* 3.4 1.4 - - - +
535A GLY 2.7 63.3 + - - +
536A VAL 3.9 0.7 - - - -
537A LYS* 3.7 39.9 - - + -
548A THR* 4.6 1.6 + - - -
549A GLY 3.9 2.3 + - - -
550A ALA* 3.2 16.7 - - + +
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Residues in contact with PHE 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 4.4 1.9 - - - +
491A GLY 5.4 0.4 - - - -
492A GLY* 3.1 3.0 - - - -
493A VAL* 2.9 69.8 + - + +
504A TYR* 1.3 87.1 - - - +
506A SER* 1.3 77.9 + - - +
533A GLU 3.2 15.3 - - - +
534A VAL* 3.9 13.2 - - + -
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Residues in contact with SER 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 2.9 25.2 + - - -
48A GLN* 5.0 5.2 - - - +
490A ARG* 5.1 4.1 - - - +
491A GLY 3.1 17.3 - - - -
492A GLY* 3.5 5.8 - - - -
505A PHE* 1.3 90.5 - - - +
507A TYR* 1.3 64.4 + - - +
508A SER* 5.2 4.3 - - - -
531A GLN* 3.8 2.3 + - - +
532A TYR* 3.7 3.6 - - - -
533A GLU* 2.9 39.7 + - - +
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Residues in contact with TYR 507 (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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489A TRP* 3.4 45.0 + + + -
490A ARG* 3.2 5.5 - - - +
491A GLY 2.9 31.6 + - - +
506A SER* 1.3 77.2 - - - +
508A SER* 1.3 65.7 + - - +
509A GLU* 2.7 42.6 + - + +
530A LYS* 3.3 18.2 - - + +
531A GLN 3.1 20.2 - - - -
532A TYR* 3.4 48.2 - + + +
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Residues in contact with SER 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 3.7 20.6 + - - -
135A PRO* 3.1 27.3 + - - +
136A VAL* 4.8 1.2 - - - -
138A VAL* 5.0 1.0 - - - +
489A TRP 3.9 6.3 - - - -
490A ARG* 3.7 19.0 - - - +
506A SER* 5.2 2.0 - - - -
507A TYR* 1.3 79.3 - - - +
509A GLU* 1.3 74.8 + - - +
529A GLY 3.8 0.3 - - - +
530A LYS* 3.8 0.2 - - - -
531A GLN* 2.8 38.6 + - - -
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Residues in contact with GLU 509 (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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135A PRO* 3.3 9.9 - - - +
137A SER* 3.4 17.8 + - - -
138A VAL* 3.6 9.4 + - - -
487A PHE* 4.6 1.2 - - - +
488A THR* 3.2 18.2 - - + -
489A TRP* 2.8 54.8 + - - +
507A TYR* 2.7 34.8 + - + +
508A SER* 1.3 83.4 + - - +
510A SER* 1.3 59.4 - - - +
529A GLY 3.1 11.7 - - - +
530A LYS* 2.9 22.9 + - - +
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Residues in contact with SER 510 (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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135A PRO* 3.6 16.6 - - - +
136A VAL 4.4 0.7 - - - -
137A SER* 2.8 22.4 - - - -
143A SER 3.7 12.6 + - - -
144A SER 4.6 0.7 - - - -
145A PRO* 3.6 18.6 - - - +
488A THR* 4.3 4.0 - - - -
509A GLU* 1.3 73.8 - - - +
511A PHE* 1.3 59.6 + - - +
528A LYS* 3.5 4.2 - - - +
529A GLY* 2.6 47.2 + - - +
530A LYS* 5.2 0.5 + - - -
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Residues in contact with PHE 511 (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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137A SER* 3.1 7.2 + - - -
141A GLY* 3.6 5.2 - - - -
142A LYS* 3.2 44.6 - - + -
143A SER 3.1 24.3 + - - -
442A GLN* 3.6 8.3 - - - -
465A ASP* 3.7 29.2 - - + -
467A ALA* 4.3 9.6 - - + -
484A ASP* 5.4 1.1 - - + -
486A GLN* 3.5 39.3 - - + +
488A THR* 3.5 22.2 - - + -
510A SER* 1.3 75.4 - - - +
512A GLU* 1.3 67.0 + - - +
513A PRO* 3.9 15.9 - - + -
526A PRO* 4.5 4.9 - - + -
527A SER 3.3 11.7 - - - +
528A LYS* 4.3 7.2 - - + +
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Residues in contact with GLU 512 (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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96A ALA 4.7 1.4 - - - +
97A ALA* 3.5 5.2 - - - +
98A GLU* 3.2 43.1 + - + +
103A ASN* 5.8 0.2 - - - -
142A LYS* 4.5 2.0 - - + -
143A SER* 3.7 8.6 - - - +
144A SER* 3.2 38.7 + - - -
145A PRO* 3.7 10.9 - - + +
511A PHE* 1.3 77.1 - - - +
513A PRO* 1.3 73.8 - - + +
514A SER* 4.7 0.2 - - - -
526A PRO* 4.0 2.2 - - - -
527A SER* 2.8 48.5 + - - +
556A LYS* 4.9 5.0 + - - -
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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