Contacts of the strand formed by residues 658 - 663 (chain A) in PDB entry 5GG4
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 TRP 658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A MET* 3.9 17.3 - - + -
566A GLN 3.0 7.9 + - - +
567A VAL* 3.3 12.8 - - + +
568A GLN 3.0 19.3 + - - -
602A LEU* 5.9 1.3 - - + -
622A LEU* 6.0 1.8 - - + -
624A PRO* 3.6 39.0 - - + +
625A MET 4.5 5.6 + - - -
638A LEU* 4.7 9.4 - - + -
648A MET* 3.7 38.6 - - + -
651A LEU* 3.8 30.5 + - + -
652A SER* 3.5 26.2 - - - +
655A GLU* 3.8 25.8 - - - +
657A PRO* 1.3 75.1 - - - +
659A THR* 1.3 66.8 + - - +
660A ILE* 3.6 26.9 - - + -
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Residues in contact with THR 659 (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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568A GLN* 3.2 28.7 + - - +
570A VAL* 4.2 5.4 - - + -
584A TYR* 3.6 18.2 - - - +
591A TYR* 3.5 30.1 + - + +
625A MET* 3.0 37.4 + - + +
633A LYS* 4.5 14.2 + - - +
655A GLU* 5.9 0.8 - - - -
657A PRO* 4.2 2.3 + - - +
658A TRP* 1.3 77.9 + - - +
660A ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 660 (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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567A VAL* 3.7 15.9 - - + -
568A GLN 2.9 8.9 + - - -
569A ILE* 3.4 16.1 - - + +
570A VAL* 3.1 24.7 + - - -
605A PHE* 4.5 11.4 - - + -
622A LEU* 3.9 26.0 - - + -
623A TRP 3.9 18.6 - - - +
624A PRO* 4.1 5.8 - - + -
625A MET* 4.5 0.2 - - - -
658A TRP* 3.6 50.7 - - + +
659A THR* 1.3 81.3 - - - +
661A PHE* 1.3 75.2 + - - +
662A LEU 3.5 0.9 + - - -
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Residues in contact with PHE 661 (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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570A VAL* 3.5 15.1 - - + +
572A GLU* 3.6 34.5 - - + -
575A PHE* 3.4 32.8 - + - -
621A ARG 3.7 2.6 - - - +
623A TRP* 2.9 67.2 + + + +
625A MET* 3.3 25.4 - - + +
635A PRO* 4.2 11.0 - - + -
660A ILE* 1.3 73.8 - - - +
662A LEU* 1.3 80.7 + - - +
663A GLU* 4.4 13.2 - - + -
686A MET* 4.8 5.2 - - - -
688A PHE* 4.0 16.2 - + - -
704A HIS* 5.1 2.0 - - - -
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Residues in contact with LEU 662 (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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569A ILE* 3.4 31.9 - - + -
570A VAL 3.1 10.0 + - - +
571A ALA* 4.1 12.8 - - + +
572A GLU* 4.2 2.6 + - - +
609A LEU* 3.8 23.3 - - + -
613A MET* 5.1 6.1 - - + -
615A PHE* 4.9 6.5 - - + -
620A ILE* 4.0 19.5 - - + -
621A ARG 3.8 1.6 - - - +
622A LEU* 3.5 27.1 - - + -
660A ILE 4.4 0.4 - - - +
661A PHE* 1.3 86.7 - - - +
663A GLU* 1.3 61.1 + - - +
664A THR* 3.2 37.4 + - + +
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Residues in contact with GLU 663 (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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572A GLU* 4.6 3.4 - - - +
619A GLN 3.7 0.5 - - - +
620A ILE* 3.2 7.8 - - - +
621A ARG* 3.0 42.1 + - + +
623A TRP* 3.2 19.1 + - + +
661A PHE* 4.1 11.6 + - + -
662A LEU* 1.3 72.8 - - - +
664A THR* 1.3 66.6 + - - +
676A LEU* 3.5 20.1 - - - +
704A HIS* 2.6 41.3 + - + +
706A TYR* 2.3 36.6 + - - -
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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