Contacts of the strand formed by residues 601 - 608 (chain A) in PDB entry 5TKD
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 THR 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A GLN* 3.4 9.5 + - - +
598A GLY* 3.1 43.2 + - - +
599A THR 3.1 9.6 + - - +
600A ARG* 1.3 85.1 - - - +
602A ASN* 1.3 69.8 + - - +
603A VAL* 4.1 8.6 - - - +
642A LYS* 4.8 5.2 - - + +
643A VAL 3.2 16.8 - - - +
644A LEU* 3.9 12.6 - - + -
645A ASP* 4.3 0.9 + - - -
655A PHE* 3.9 23.1 - - + -
761A GLY* 6.1 2.0 - - - -
762A VAL* 5.0 1.8 - - + +
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Residues in contact with ASN 602 (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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594A HIS* 2.9 22.0 + - - +
596A GLY 3.7 2.7 - - - -
597A GLN* 3.0 25.5 + - - +
601A THR* 1.3 77.2 + - - +
603A VAL* 1.3 61.7 + - - +
604A TYR* 3.6 27.8 + - + +
641A LEU 3.5 1.9 - - - +
642A LYS* 3.7 0.3 - - - -
643A VAL* 2.8 37.6 + - + +
645A ASP* 3.9 15.0 + - - -
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Residues in contact with VAL 603 (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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594A HIS* 3.7 4.0 - - - -
595A LEU* 2.7 37.2 + - + -
596A GLY 2.8 18.4 + - - +
598A GLY* 4.6 1.6 - - - +
601A THR* 4.1 15.5 - - - +
602A ASN* 1.3 76.8 - - - +
604A TYR* 1.3 53.7 + - - +
640A VAL* 3.5 31.0 - - + -
641A LEU 3.3 2.9 - - - +
642A LYS* 4.0 21.5 - - + -
901A 7GL 3.6 43.1 - - + +
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Residues in contact with TYR 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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591A GLN* 3.4 36.9 + - + -
592A LEU 3.6 15.9 - - - +
593A SER 3.3 6.3 - - - +
594A HIS* 3.6 35.3 - + + -
595A LEU* 3.8 6.1 - - - +
602A ASN* 3.6 37.5 + - + +
603A VAL* 1.3 74.6 - - - +
605A GLU* 1.3 68.9 + - - +
640A VAL* 3.4 6.4 - - - +
641A LEU* 2.8 35.5 + - + +
643A VAL* 3.8 22.9 - - + -
679A ARG* 6.0 0.2 - - - -
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Residues in contact with GLU 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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591A GLN* 4.1 0.7 - - - -
592A LEU* 2.8 35.7 + - + +
593A SER* 2.9 24.6 + - - +
595A LEU* 3.7 19.8 - - + +
604A TYR* 1.3 79.0 - - - +
606A GLY* 1.3 60.7 + - - +
607A ARG* 3.3 31.9 + - - +
638A ARG* 3.6 8.5 - - - -
639A VAL 3.7 4.3 - - - +
641A LEU* 4.5 0.6 - - - +
689A TYR* 3.6 33.2 + - + -
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Residues in contact with GLY 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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590A THR 3.0 14.4 - - - -
592A LEU* 4.1 4.0 - - - -
604A TYR 3.8 0.4 + - - -
605A GLU* 1.3 76.8 - - - +
607A ARG* 1.3 79.4 + - - -
639A VAL* 2.9 39.3 + - - +
641A LEU* 4.2 6.3 - - - +
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Residues in contact with ARG 607 (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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589A ILE* 3.3 9.0 - - - +
590A THR* 3.0 44.4 + - + +
592A LEU* 3.4 25.4 - - + +
605A GLU* 3.3 21.4 + - - +
606A GLY* 1.3 90.4 + - - -
608A LEU* 1.3 61.8 + - - +
609A ARG 4.2 0.4 - - - -
637A LEU 3.3 15.9 - - - +
638A ARG* 3.2 30.6 - - - +
639A VAL* 3.9 3.0 - - - +
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Residues in contact with LEU 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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582A HIS* 6.4 0.7 - - + -
584A VAL* 3.9 20.2 - - + -
588A GLU* 3.4 16.4 - - + +
589A ILE* 3.8 16.2 - - + -
607A ARG* 1.3 76.3 - - - +
609A ARG* 1.3 72.8 + - - +
637A LEU* 2.8 37.2 + - + +
639A VAL* 3.8 21.1 - - + -
674A HIS* 3.9 39.5 - - + +
686A VAL* 4.4 3.6 - - + -
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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