Contacts of the strand formed by residues 527 - 538 (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 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A PRO* 5.8 0.7 - - - +
511A PHE* 3.3 3.1 - - - +
512A GLU* 2.8 49.0 + - - +
514A SER* 6.0 0.4 - - - -
526A PRO* 1.3 75.0 - - - +
528A LYS* 1.3 65.0 + - - +
556A LYS* 3.6 27.6 - - - +
557A THR 3.2 14.8 - - - -
558A ASN* 3.5 13.9 - - - -
559A ASN* 4.9 0.4 - - - -
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Residues in contact with LYS 528 (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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145A PRO* 5.4 2.0 - - - -
486A GLN* 3.5 32.0 + - - +
487A PHE 5.6 2.7 + - - +
510A SER* 3.6 4.7 - - - +
511A PHE* 4.3 7.6 - - + +
526A PRO* 4.8 7.0 - - + +
527A SER* 1.3 83.3 - - - +
529A GLY* 1.3 59.2 + - - +
530A LYS* 4.1 24.5 - - - +
555A THR 3.4 0.9 - - - +
556A LYS* 3.0 12.2 - - - +
557A THR* 2.9 47.1 + - - +
558A ASN* 5.8 1.1 - - + -
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Residues in contact with GLY 529 (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* 4.4 3.6 - - - -
145A PRO* 4.2 12.6 - - - -
508A SER 4.4 0.2 - - - -
509A GLU* 3.1 26.9 - - - +
510A SER* 2.6 33.5 + - - +
528A LYS* 1.3 72.2 - - - +
530A LYS* 1.3 69.8 + - - +
531A GLN 4.3 0.4 - - - -
555A THR 3.4 3.8 - - - -
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Residues in contact with LYS 530 (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 6.0 0.2 + - - -
507A TYR* 3.3 22.0 - - + +
508A SER 3.8 1.8 - - - -
509A GLU* 2.9 30.9 + - + +
510A SER 5.2 0.4 + - - -
528A LYS* 4.1 28.0 - - - +
529A GLY* 1.3 83.1 + - - +
531A GLN* 1.3 59.1 + - - +
532A TYR* 5.6 6.2 - - + -
553A ASN 3.6 1.8 - - - +
554A LEU* 3.3 2.7 - - - +
555A THR* 2.5 58.4 + - + +
557A THR* 5.2 8.7 - - + +
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Residues in contact with GLN 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 3.9 15.6 - - - +
93A ARG* 2.4 44.0 + - - +
133A ARG 4.0 1.2 + - - -
134A GLY* 3.4 22.7 - - - -
135A PRO* 3.4 20.3 - - + +
506A SER* 3.8 2.6 + - - +
507A TYR* 3.1 10.7 - - - -
508A SER* 2.8 40.7 + - - +
530A LYS* 1.3 72.0 - - - +
532A TYR* 1.3 73.5 + - - +
533A GLU* 4.1 11.7 + - - +
552A TYR* 3.9 6.3 - - + -
553A ASN 3.1 10.5 - - - +
554A LEU* 3.5 11.0 - - + +
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Residues in contact with TYR 532 (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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506A SER 3.7 3.6 - - - -
507A TYR* 3.4 41.6 - + + -
530A LYS* 5.6 5.4 - - + -
531A GLN* 1.3 75.1 - - - +
533A GLU* 1.3 60.7 + - - +
534A VAL* 5.2 2.7 - - + -
552A TYR* 3.1 4.3 - - - +
553A ASN* 2.7 55.3 + - + +
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Residues in contact with GLU 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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47A PRO 5.6 0.2 - - - +
48A GLN* 5.0 2.2 - - + -
49A SER* 2.9 27.0 + - - -
93A ARG* 2.2 43.6 + - - -
504A TYR* 2.8 32.5 + - + -
505A PHE* 3.2 2.6 - - - +
506A SER* 2.9 42.4 + - - +
531A GLN* 4.0 13.6 - - - +
532A TYR* 1.3 75.1 - - - +
534A VAL* 1.3 76.2 - - - +
550A ALA* 3.9 6.0 - - + +
551A VAL 3.5 11.9 - - - +
552A TYR* 3.9 5.6 - - + +
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Residues in contact with VAL 534 (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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504A TYR* 3.4 9.2 - - - +
505A PHE* 3.9 14.8 - - + +
532A TYR* 5.2 2.7 - - + -
533A GLU* 1.3 85.9 - - - +
535A GLY* 1.3 63.5 + - - +
550A ALA* 3.5 1.7 - - - +
551A VAL* 2.9 44.9 + - + +
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Residues in contact with GLY 535 (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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504A TYR* 2.7 43.0 + - - +
534A VAL* 1.3 80.3 - - - +
536A VAL* 1.3 68.0 + - - +
549A GLY 3.3 15.0 - - - -
550A ALA* 4.0 2.9 - - - -
551A VAL* 5.1 1.8 - - - -
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Residues in contact with VAL 536 (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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501A VAL* 5.3 8.3 - - + -
502A THR 3.2 9.6 - - - +
503A PRO* 3.6 21.3 - - + -
504A TYR* 4.1 0.2 - - - -
535A GLY* 1.3 82.6 - - - +
537A LYS* 1.3 68.6 + - - +
538A TYR* 5.1 3.6 - - + +
547A VAL 4.1 0.7 - - - +
548A THR* 3.5 2.1 - - - -
549A GLY* 2.9 33.8 + - - +
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Residues in contact with LYS 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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43A ILE* 2.8 27.6 + - + +
44A GLN* 4.1 4.7 - - - +
46A VAL* 2.3 35.2 + - - +
48A GLN 3.0 18.6 + - - -
49A SER* 4.9 4.3 - - - +
50A ILE* 4.3 10.2 - - - +
501A VAL* 4.7 0.2 - - - -
502A THR* 2.5 57.8 + - - +
504A TYR* 3.7 27.8 - - + -
536A VAL* 1.3 77.6 - - - +
538A TYR* 1.3 60.0 + - - +
539A VAL* 3.4 14.8 + - + -
547A VAL 3.6 3.6 - - - +
548A THR* 3.7 19.3 - - - +
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Residues in contact with TYR 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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499A ASN* 3.9 11.8 + - - -
500A GLY 2.5 33.7 - - - +
501A VAL* 4.5 9.6 - - + +
536A VAL* 4.2 4.5 - - + +
537A LYS* 1.3 70.5 - - - +
539A VAL* 1.3 59.6 + - - +
540A PRO* 3.2 28.8 - - + +
542A ASP* 4.8 0.7 + - - -
543A ARG* 4.4 14.3 + - - -
545A ILE* 2.9 38.9 - - + +
546A VAL* 3.4 2.1 - - - -
547A VAL* 2.7 56.2 + - + +
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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