Contacts of the strand formed by residues 603 - 612 (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 SER 603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A ASN* 3.6 26.2 - - - -
557A ILE* 4.0 2.3 - - - +
558A THR* 2.6 49.1 + - - +
560A TYR* 3.8 11.7 + - - -
598A LEU* 4.6 1.9 - - - +
599A LEU 4.8 1.5 + - - +
601A GLN* 4.1 11.4 + - - +
602A ALA* 1.3 74.9 + - - +
604A LEU* 1.3 69.5 + - - +
625A THR 3.3 5.8 - - - -
626A VAL* 4.2 8.3 - - - -
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Residues in contact with LEU 604 (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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533A PHE* 3.6 31.6 - - + -
556A ASN 3.5 2.9 - - - -
557A ILE* 3.9 19.3 - - + -
558A THR* 4.4 3.1 - - - -
568A PHE* 3.9 21.1 - - + -
594A TYR* 4.4 6.1 - - + -
598A LEU* 3.4 25.4 - - + -
603A SER* 1.3 85.3 - - - +
605A HIS* 1.3 60.3 + - - +
606A PHE* 4.4 6.5 - - + -
624A SER* 3.0 6.4 - - - -
625A THR* 2.5 57.0 + - + +
627A LEU* 4.1 17.7 - - + -
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Residues in contact with HIS 605 (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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339A PHE* 6.2 0.2 - - - -
371A ASN* 5.6 0.9 - - - +
459A HIS* 5.8 1.0 + - - -
554A SER 3.9 0.3 - - - +
555A ALA* 3.4 2.8 - - - -
556A ASN* 2.7 48.7 + - + +
558A THR* 3.7 26.1 + - + +
562A GLY* 5.8 0.8 + - - -
604A LEU* 1.3 75.8 - - - +
606A PHE* 1.3 65.3 + - - +
607A PHE* 3.7 32.5 - + - -
622A GLN* 2.7 37.1 + - - +
623A LYS 2.8 26.2 + - - -
624A SER* 3.4 16.8 - - - +
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Residues in contact with PHE 606 (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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522A PHE* 3.5 30.5 - + + -
524A VAL* 4.6 13.2 - - + -
533A PHE* 4.1 21.3 - + - -
535A LEU* 3.9 24.2 - - + -
553A LEU* 4.0 3.8 - - + -
554A SER 3.4 1.8 - - - +
555A ALA* 3.5 30.7 - - + -
568A PHE* 3.9 16.8 - + - -
589A ILE* 4.6 4.5 - - + -
604A LEU* 4.4 10.5 - - + -
605A HIS* 1.3 76.5 + - - +
607A PHE* 1.3 64.5 + - - +
608A VAL* 4.8 1.1 - - + -
622A GLN* 3.0 27.4 - - - +
623A LYS* 2.9 20.9 + - + +
625A THR* 4.1 26.7 - - - -
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Residues in contact with PHE 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 3.8 33.4 - - + -
360A VAL* 3.7 37.0 - - + -
365A THR* 5.1 7.4 - - + -
441A TYR* 4.2 7.4 - + - -
552A TYR 3.8 0.4 - - - +
553A LEU* 3.4 0.5 - - - -
554A SER* 2.8 50.3 + - - +
556A ASN* 4.9 6.7 - - - -
605A HIS* 3.7 23.3 - + - -
606A PHE* 1.3 72.3 - - - +
608A VAL* 1.3 70.5 + - - +
609A THR* 4.0 2.5 - - + -
620A ALA* 6.3 0.4 - - + -
621A LYS 3.7 3.6 - - - -
622A GLN* 3.6 37.9 - - + -
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Residues in contact with VAL 608 (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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520A MET* 3.7 24.0 - - + +
522A PHE* 3.4 50.3 - - + -
535A LEU* 5.0 0.7 - - + -
537A ILE* 4.6 15.9 - - + -
551A ALA* 6.5 0.4 - - + -
552A TYR 3.3 8.3 - - - +
553A LEU* 4.1 20.0 - - + -
607A PHE* 1.3 81.9 - - - +
609A THR* 1.3 62.9 + - - +
620A ALA* 3.7 1.6 - - - -
621A LYS* 2.7 36.2 + - + +
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Residues in contact with THR 609 (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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354A LEU* 4.9 5.2 - - - +
358A GLY* 2.5 36.2 + - - +
359A ASN* 4.4 1.6 - - - -
360A VAL* 4.1 24.0 - - + +
520A MET* 4.9 0.5 - - - +
551A ALA* 3.5 1.9 - - - +
552A TYR* 2.9 42.8 + - + +
554A SER* 5.9 2.0 - - - +
607A PHE* 5.1 2.5 - - - -
608A VAL* 1.3 77.7 - - - +
610A ALA* 1.3 70.3 + - - +
618A VAL* 4.6 8.4 - - - +
619A LEU 3.4 7.1 + - - -
620A ALA* 4.4 8.5 - - - +
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Residues in contact with ALA 610 (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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358A GLY* 6.0 0.2 - - - -
520A MET* 4.2 14.6 - - - -
539A PHE* 4.2 3.6 - - + -
549A ILE* 4.0 13.0 - - + -
550A THR 3.4 12.6 - - - +
551A ALA* 3.9 13.5 - - + -
552A TYR* 4.7 1.1 - - - -
609A THR* 1.3 85.0 + - - +
611A ARG* 1.3 61.0 + - - +
612A ILE 4.1 0.2 + - - -
617A ASP 3.8 0.9 - - - +
618A VAL* 3.7 2.8 - - - -
619A LEU* 2.8 46.6 + - + +
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Residues in contact with ARG 611 (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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356A GLU 4.0 10.1 + - - -
357A ASP* 2.9 28.3 + - - +
358A GLY* 5.3 2.6 - - - -
549A ILE* 2.9 20.6 - - - +
550A THR* 3.0 35.5 + - - +
552A TYR* 3.5 22.4 + - + -
610A ALA* 1.3 72.6 - - - +
612A ILE* 1.3 68.7 + - - +
613A ASN* 2.7 33.1 + - - +
616A ARG* 4.6 14.1 - - - +
617A ASP 3.7 7.0 - - - +
618A VAL* 4.7 9.0 - - + +
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Residues in contact with ILE 612 (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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516A SER* 3.7 9.2 - - - +
518A VAL* 4.0 9.4 - - + -
547A TYR* 3.8 28.7 - - + -
548A THR 3.7 5.2 - - - +
549A ILE* 3.7 28.3 - - + -
611A ARG* 1.3 72.6 - - - +
613A ASN* 1.3 61.1 + - - +
614A GLU 3.1 0.7 + - - +
615A THR* 3.0 24.9 - - - +
616A ARG* 2.7 33.8 + - - -
617A ASP* 2.8 28.5 + - + +
619A LEU* 3.5 35.7 - - + -
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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