Contacts of the strand formed by residues 617 - 626 (chain B) 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 ASP 617 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512B MET 5.3 0.2 - - - +
513B LYS* 3.7 18.7 + - + +
514B SER* 3.8 9.8 + - - -
515B ARG* 3.0 25.2 + - - +
516B SER* 2.9 26.5 + - - -
610B ALA 3.8 0.3 - - - +
611B ARG* 4.6 0.4 - - - -
612B ILE* 3.1 33.0 + - + +
615B THR* 3.0 26.9 + - - +
616B ARG* 1.3 77.5 - - - +
618B VAL* 1.3 63.0 + - - +
619B LEU* 3.5 3.3 + - + +
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Residues in contact with VAL 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 3.9 24.5 - - + -
357B ASP 6.0 0.4 - - - +
358B GLY* 5.0 11.7 - - - +
443B THR* 5.4 1.1 - - - +
453B GLU* 3.1 34.8 - - + +
454B ASN* 4.2 7.3 - - + +
513B LYS* 3.1 32.3 - - - +
609B THR* 4.8 3.6 - - - -
610B ALA 3.0 19.1 - - - +
611B ARG* 4.6 8.3 - - + +
616B ARG 4.2 5.4 - - - +
617B ASP* 1.3 70.7 - - - +
619B LEU* 1.3 70.4 + - - +
620B ALA* 5.2 1.1 - - + -
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Residues in contact with LEU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ASN* 5.9 1.1 - - - -
513B LYS* 5.2 2.9 - - + -
515B ARG* 3.2 41.5 - - + +
518B VAL* 3.7 25.8 - - + +
520B MET* 3.8 37.0 - - + +
539B PHE* 5.5 1.3 - - + -
609B THR* 3.1 2.4 - - - -
610B ALA* 2.7 36.3 + - + +
612B ILE* 3.8 22.4 - - + -
617B ASP* 3.9 10.5 - - + +
618B VAL* 1.3 84.2 - - - +
620B ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 5.4 0.4 - - + -
441B TYR* 3.7 45.0 + - + -
454B ASN* 4.9 10.8 + - + +
456B ASP* 5.7 0.5 - - - +
520B MET* 4.4 1.1 - - - +
608B VAL 3.4 7.2 - - - -
609B THR* 3.7 13.9 - - + -
618B VAL* 5.2 4.5 - - + +
619B LEU* 1.3 77.9 - - - +
621B LYS* 1.3 78.6 + - - +
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Residues in contact with LYS 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B TYR* 4.5 5.1 - - - -
456B ASP* 5.0 14.8 - - - +
515B ARG* 4.8 11.3 - - - +
519B ASP* 5.2 1.6 + - - -
520B MET* 3.9 30.0 + - + +
521B ASP* 4.4 16.2 + - - +
522B PHE* 4.0 20.6 - - + -
540B ARG* 5.4 1.4 - - - +
607B PHE* 3.8 2.3 - - - -
608B VAL* 2.9 33.2 + - + +
609B THR* 5.5 0.3 - - - +
620B ALA* 1.3 85.6 - - - +
622B GLN* 1.3 68.5 + - - +
623B LYS* 5.2 8.5 - - - +
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Residues in contact with GLN 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ILE* 4.0 10.2 - - - +
369B VAL* 4.9 8.1 - - - +
439B LEU* 3.6 16.0 - - + +
441B TYR* 2.9 25.3 + - - +
456B ASP* 5.8 1.3 - - - +
459B HIS* 3.8 35.3 + - + +
522B PHE* 4.3 3.1 - - - -
605B HIS* 2.6 30.0 + - + +
606B PHE 3.1 17.9 - - - +
607B PHE* 3.8 19.7 - - + -
621B LYS* 1.3 80.5 - - - +
623B LYS* 1.3 73.3 + - - +
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Residues in contact with LYS 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ASN* 4.3 22.2 - - - +
339B PHE* 5.3 4.3 - - + -
459B HIS* 4.9 7.2 - - + -
521B ASP* 3.3 24.1 + - - -
522B PHE* 3.4 45.6 + - + +
523B GLU* 5.2 3.6 - - - +
524B VAL* 4.9 11.2 - - + +
605B HIS* 3.2 5.7 - - - -
606B PHE* 2.9 28.8 + - - -
621B LYS* 5.2 8.5 - - - +
622B GLN* 1.3 83.7 + - - +
624B SER* 1.3 70.3 + - - +
625B THR* 6.2 0.7 - - + -
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Residues in contact with SER 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B GLU* 3.2 26.3 - - - +
218B ASN* 4.7 1.8 + - - +
339B PHE* 4.5 13.4 - - - -
369B VAL* 6.1 0.9 - - - +
371B ASN* 3.5 30.2 + - - -
558B THR* 5.7 0.7 - - - -
603B SER* 5.4 0.2 - - - -
604B LEU 3.0 14.6 - - - -
605B HIS* 3.0 26.3 - - - +
606B PHE* 4.7 1.3 - - - -
623B LYS* 1.3 76.8 - - - +
625B THR* 1.3 71.4 + - - +
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Residues in contact with THR 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B GLU* 3.8 12.1 - - - +
218B ASN* 6.1 1.1 - - - +
524B VAL* 3.5 45.8 - - + +
526B ASN* 5.5 9.9 - - + -
533B PHE* 4.9 2.6 - - - -
602B ALA 3.8 0.2 - - - +
603B SER* 3.0 4.6 - - - -
604B LEU* 2.8 41.3 + - - +
606B PHE* 3.5 18.6 - - + -
623B LYS* 5.5 1.6 - - + -
624B SER* 1.3 81.7 - - - +
626B VAL* 1.3 66.3 + - - +
627B LEU* 5.5 1.8 - - - +
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Residues in contact with VAL 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLY* 4.1 25.4 - - - +
216B GLU* 4.2 6.8 + - + -
219B ASP* 3.4 36.7 + - + +
221B LYS* 4.0 21.8 - - + +
371B ASN* 4.9 2.5 - - - +
526B ASN* 5.1 4.5 - - - +
527B ALA 4.4 4.0 + - - +
601B GLN* 4.1 13.9 - - + +
602B ALA 3.2 4.7 - - - +
603B SER* 3.8 18.8 - - - -
625B THR* 1.3 79.4 - - - +
627B LEU* 1.3 67.4 + - - +
628B THR* 3.5 2.8 + - - -
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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