Contacts of the strand formed by residues 564 - 577 (chain A) in PDB entry 1GGT
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 PRO 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A SER* 5.2 4.5 - - - +
556A ASN* 3.9 26.0 - - + +
557A ILE 3.5 8.3 - - - +
558A THR* 4.0 9.0 - - + -
559A PHE* 4.3 2.9 - - - -
562A GLY 3.1 8.5 - - - +
563A VAL* 1.3 96.9 - - + +
565A LYS* 1.3 60.7 + - - +
566A ALA 4.5 0.2 - - - +
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Residues in contact with LYS 565 (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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557A ILE* 2.9 9.8 + - + +
559A PHE* 4.1 10.8 - - + -
563A VAL 4.0 0.2 + - - -
564A PRO* 1.3 75.4 - - - +
566A ALA* 1.3 66.7 + - + +
597A GLN* 4.0 42.0 + - - +
598A LEU 5.5 0.4 - - - -
599A LEU* 3.6 40.2 - - + -
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Residues in contact with ALA 566 (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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556A ASN* 3.2 9.9 + - - +
557A ILE* 2.7 38.6 + - + +
564A PRO* 3.7 1.2 - - - +
565A LYS* 1.3 87.8 - - + +
567A GLU* 1.3 60.1 + - - +
568A PHE 3.6 1.0 + - - -
597A GLN* 3.5 36.8 - - + +
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Residues in contact with GLU 567 (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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554A SER* 2.7 27.8 + - - +
555A ALA 3.5 11.0 - - - +
556A ASN* 3.5 12.6 - - - +
566A ALA* 1.3 70.4 - - - +
568A PHE* 1.3 62.3 + - - +
569A LYS 3.5 20.4 + - - +
570A LYS* 2.7 39.2 + - + +
597A GLN* 4.9 2.3 + - - -
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Residues in contact with PHE 568 (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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555A ALA* 2.8 46.9 + - + -
556A ASN 3.4 17.9 - - - -
557A ILE* 3.7 25.1 - - + -
566A ALA 3.6 1.2 + - - -
567A GLU* 1.3 73.6 - - - +
569A LYS* 1.3 64.6 + - + +
589A ILE* 3.4 28.7 - - + -
593A GLU* 2.9 62.5 - - + +
594A TYR* 3.8 23.8 - + + -
597A GLN* 4.5 3.8 - - - +
604A LEU* 3.9 25.1 - - + -
606A PHE* 3.9 12.1 - + - -
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Residues in contact with LYS 569 (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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553A LEU* 3.5 5.4 - - + +
555A ALA* 3.0 41.5 + - + +
567A GLU* 3.3 10.0 + - - +
568A PHE* 1.3 83.1 - - + +
570A LYS* 1.3 63.6 + - - +
571A GLU* 5.4 9.9 - - + +
587A VAL* 5.2 6.7 - - + -
588A LEU 4.1 17.3 - - - +
589A ILE* 4.1 22.0 - - + +
590A GLN* 3.6 26.3 + - - +
593A GLU* 3.6 28.6 - - + +
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Residues in contact with LYS 570 (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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359A ASN* 3.9 29.7 + - - +
360A VAL 5.0 10.1 + - - +
552A TYR* 6.3 0.2 - - + -
553A LEU 3.2 6.3 - - - +
554A SER* 4.4 7.7 + - - +
567A GLU* 2.7 41.6 + - + +
569A LYS* 1.3 78.1 - - - +
571A GLU* 1.3 73.5 + - - +
572A THR* 5.2 0.3 + - - -
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Residues in contact with GLU 571 (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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552A TYR* 3.3 7.3 - - - +
553A LEU* 3.0 54.6 + - + +
569A LYS* 4.3 11.0 - - + +
570A LYS* 1.3 85.9 - - - +
572A THR* 1.3 70.6 + - - +
573A PHE* 3.3 27.0 - - + -
587A VAL* 4.8 13.4 - - + +
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Residues in contact with THR 572 (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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550A THR* 5.1 5.6 - - + -
551A ALA 2.9 9.0 - - - +
552A TYR* 3.2 39.9 - - + -
570A LYS* 5.2 0.4 + - + -
571A GLU* 1.3 81.4 - - - +
573A PHE* 1.3 73.3 + - - +
574A ASP* 6.1 0.7 - - - -
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Residues in contact with PHE 573 (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 ILE* 3.9 30.5 - - + -
539A PHE* 4.4 3.1 - + - -
550A THR* 3.0 8.7 - - - +
551A ALA* 2.6 54.7 + - + +
552A TYR 5.7 0.7 - - - -
553A LEU* 4.6 14.1 - - + -
571A GLU* 3.3 40.6 - - + -
572A THR* 1.3 94.0 - - - +
574A ASP* 1.3 67.8 + - - +
575A VAL* 4.9 4.0 - - + -
585A GLU* 4.0 31.2 - - + -
586A ALA 5.9 0.7 - - - -
587A VAL* 4.7 6.7 - - + -
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Residues in contact with ASP 574 (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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548A THR* 5.4 5.6 - - + +
549A ILE 3.0 6.3 - - - +
550A THR* 3.1 34.5 + - - +
572A THR* 6.1 0.3 - - - -
573A PHE* 1.3 77.0 - - - +
575A VAL* 1.3 64.5 + - - +
585A GLU* 6.0 0.2 - - - -
613A ASN* 4.4 5.9 + - - -
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Residues in contact with VAL 575 (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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539A PHE* 4.2 28.0 - - + -
548A THR* 3.0 9.9 - - - +
549A ILE* 2.6 73.6 + - + +
551A ALA* 5.4 0.2 - - + -
573A PHE* 4.9 4.5 - - + -
574A ASP* 1.3 79.0 - - - +
576A THR* 1.3 65.3 + - - +
577A LEU* 3.9 9.2 - - + -
583A LYS* 4.6 9.9 - - + -
585A GLU* 3.3 31.2 - - + +
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Residues in contact with THR 576 (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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546A ARG* 5.6 9.0 - - + +
547A TYR 3.0 11.2 - - - +
548A THR* 3.9 12.8 - - + +
574A ASP 5.4 0.3 - - - -
575A VAL* 1.3 76.8 + - - +
577A LEU* 1.3 62.6 + - - +
578A GLU* 2.6 30.7 - - + +
583A LYS* 3.2 14.4 - - - +
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Residues in contact with LEU 577 (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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518A VAL* 3.6 28.5 - - + -
539A PHE* 4.2 14.1 - - + +
540A ARG 4.4 0.2 - - - +
541A ASN* 2.9 47.7 + - + +
545A ASN 3.0 1.0 - - - +
546A ARG* 4.1 0.2 - - - -
547A TYR* 2.6 41.3 + - + -
549A ILE* 3.6 23.8 - - + -
575A VAL* 3.9 11.7 - - + -
576A THR* 1.3 77.0 - - - +
578A GLU* 1.3 60.0 + - - +
583A LYS* 3.4 28.5 - - + +
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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