Contacts of the strand formed by residues 715 - 722 (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 ARG 715 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A ASN* 3.1 33.5 + - - -
282A ILE 4.2 11.5 + - - -
283A TYR* 3.3 11.3 - - - -
288A PRO* 3.9 18.4 - - - +
290A SER* 4.4 12.6 - - - -
600A GLU* 3.3 50.4 + - + +
629A ILE* 5.6 0.7 - - - +
709A MET* 3.7 8.1 - - - -
710A SER* 3.5 21.2 + - - +
711A SER 3.2 21.5 + - - -
712A ASP* 3.6 18.8 + - - +
714A LEU* 1.3 88.0 - - - +
716A HIS* 1.3 73.5 + - + +
717A VAL* 3.5 3.6 - - - +
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Residues in contact with HIS 716 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A TYR* 3.3 40.3 + + - -
290A SER* 2.6 36.3 + - - -
315A TRP* 3.9 12.1 - + - -
372A TYR* 4.5 1.0 + - - -
600A GLU 3.7 10.1 - - - +
601A GLN* 3.4 43.3 + - + +
629A ILE* 4.3 14.4 - - - +
709A MET 3.7 4.6 + - - -
715A ARG* 1.3 83.1 - - + +
717A VAL* 1.3 62.4 + - - +
718A TYR* 3.5 31.9 + + - -
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Residues in contact with VAL 717 (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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629A ILE* 4.2 19.7 - - + -
630A PRO* 4.5 14.4 - - + +
632A ILE* 4.4 5.8 - - + +
652A PHE* 4.2 10.8 - - + -
655A PRO* 6.2 0.2 - - + -
709A MET* 3.2 53.3 + - + +
714A LEU* 3.8 36.8 - - + -
715A ARG 4.2 1.8 - - - -
716A HIS* 1.3 83.0 - - - +
718A TYR* 1.3 69.7 + - - +
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Residues in contact with TYR 718 (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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214A TYR* 3.4 28.7 - + - -
223A ARG* 3.5 54.0 + - + +
290A SER* 2.8 34.0 + - - -
315A TRP* 4.8 1.4 + - - -
629A ILE* 6.0 0.6 - - - +
631A GLU* 3.2 12.2 - - - +
632A ILE* 2.8 27.9 + - - -
706A ILE* 6.0 1.6 - - + -
707A ALA 3.6 7.9 - - - +
708A SER* 3.6 19.5 - - - -
716A HIS* 3.4 43.7 + + - -
717A VAL* 1.3 80.8 - - - +
719A GLY* 1.3 60.9 + - - +
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Residues in contact with GLY 719 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A GLU* 4.8 3.1 - - - -
632A ILE* 3.7 22.4 - - - -
634A ILE* 3.7 7.4 - - - -
706A ILE* 3.4 5.0 - - - +
707A ALA 2.7 35.5 + - - +
718A TYR* 1.3 80.0 - - - +
720A GLU* 1.3 60.6 + - - +
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Residues in contact with GLU 720 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A THR* 4.7 5.8 + - - +
223A ARG* 4.2 7.3 - - - -
224A SER* 3.2 40.8 + - - +
472A ASP* 4.0 8.3 - - - +
632A ILE 5.4 1.2 - - - +
634A ILE* 3.8 8.5 + - - +
704A LYS* 3.6 19.0 + - + +
705A LEU 3.2 13.5 - - - +
706A ILE* 4.7 0.9 - - + -
719A GLY* 1.3 75.7 - - - +
721A LEU* 1.3 66.9 + - - +
722A ASP* 4.7 1.0 - - - +
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A ILE* 3.4 47.6 - - + +
635A LYS* 3.9 0.4 - - - -
636A VAL* 3.5 39.3 - - + +
704A LYS* 3.1 2.3 - - - -
705A LEU* 2.7 39.5 + - + +
720A GLU* 1.3 77.7 - - - +
722A ASP* 1.3 77.7 + - - +
723A VAL* 3.8 3.4 + - + +
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Residues in contact with ASP 722 (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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472A ASP* 3.8 5.7 - - - +
702A HIS* 3.2 29.5 + - + +
703A ARG 3.6 4.3 - - - -
704A LYS* 2.6 41.0 + - - +
720A GLU* 4.7 2.3 - - - +
721A LEU* 1.3 84.2 + - - +
723A VAL* 1.3 64.8 + - - +
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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