Contacts of the helix formed by residues 572 - 583 (chain B) in PDB entry 6T2C
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 572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519B GLU* 3.3 23.6 + - - -
559B TYR 3.3 26.8 + - - -
560B ARG* 3.7 22.4 - - + +
561B CYS* 4.5 5.0 - - - +
570B THR* 3.2 2.4 + - - -
571B ARG* 1.3 86.2 - - + +
573B THR* 1.3 59.1 + - - +
574B LYS 3.2 3.8 + - - -
575B SER* 3.3 5.4 + - - -
576B ILE* 2.9 38.6 + - + +
592B ALA 3.0 26.7 + - - -
593B ASP* 5.1 0.2 + - - -
664B HIS* 4.4 10.3 + - - -
51C MET* 5.0 2.1 - - - +
93C PRO* 3.7 36.9 + - + +
94C ASN* 3.8 13.7 - - - +
96C VAL* 5.3 3.2 - - - +
97C THR* 3.3 26.1 + - - +
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Residues in contact with THR 573 (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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560B ARG 6.0 0.2 - - - -
562B HIS* 6.4 2.0 - - + -
563B ARG 5.5 1.1 - - - +
564B GLY 6.1 0.9 - - - +
566B THR* 4.7 13.0 - - - +
568B LEU* 3.9 21.1 - - + +
569B GLU* 4.0 12.6 - - - +
570B THR* 2.5 44.2 + - - +
572B ARG* 1.3 74.1 - - - +
574B LYS* 1.3 58.4 + - - +
576B ILE* 4.2 12.3 - - + -
577B LYS* 2.9 33.6 + - + +
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Residues in contact with LYS 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B GLU* 3.9 23.3 - - - +
570B THR 5.5 3.4 - - - +
571B ARG 5.1 1.8 + - - +
572B ARG 3.2 1.0 + - - -
573B THR* 1.3 79.1 - - - +
575B SER* 1.3 58.9 + - - +
577B LYS* 3.2 5.8 + - - +
578B ARG* 3.0 31.4 + - - +
73C ASP* 3.5 43.6 + - + +
75C ASN* 4.4 13.9 - - - +
94C ASN* 5.1 0.4 - - - +
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Residues in contact with SER 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ARG 3.3 3.5 + - - -
574B LYS* 1.3 75.2 - - - +
576B ILE* 1.3 61.0 + - - +
578B ARG* 3.9 3.2 - - - +
579B LEU* 2.9 30.0 + - - +
71C ASP* 4.2 8.5 + - - -
73C ASP* 4.0 7.8 + - - -
94C ASN* 3.9 21.6 + - - -
97C THR* 3.7 27.5 - - - +
98C TRP* 4.9 0.9 + - - -
101C ARG* 3.8 30.3 + - - +
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Residues in contact with ILE 576 (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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560B ARG 3.9 1.8 - - - +
561B CYS* 3.9 30.1 - - + -
562B HIS 3.8 17.3 - - - +
563B ARG 4.6 1.8 - - - +
564B GLY* 4.4 13.5 - - - -
572B ARG* 2.9 47.4 + - + +
573B THR* 4.2 10.5 - - + +
575B SER* 1.3 77.2 - - - +
577B LYS* 1.3 56.5 + - - +
579B LEU* 3.8 3.7 - - - +
580B TRP* 2.9 29.2 + - + +
592B ALA 4.7 2.5 - - - +
593B ASP 4.3 18.9 - - - +
594B GLY* 4.4 1.3 - - - +
97C THR* 4.0 17.7 - - + +
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Residues in contact with LYS 577 (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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564B GLY 3.6 24.4 + - - +
565B ASP* 4.5 9.3 - - - +
566B THR 4.9 4.6 + - - +
573B THR* 2.9 25.0 + - + +
574B LYS* 3.4 6.5 - - - +
576B ILE* 1.3 78.9 - - - +
578B ARG* 1.3 59.5 + - + +
580B TRP* 3.3 7.4 + - + +
581B THR* 3.0 52.3 + - + +
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Residues in contact with ARG 578 (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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574B LYS 3.0 16.0 + - - +
575B SER 3.4 4.0 + - - +
577B LYS* 1.3 78.1 - - + +
579B LEU* 1.3 58.4 + - - +
581B THR* 3.2 7.4 + - - -
582B GLU* 3.0 56.4 + - - +
72C GLU* 4.2 17.5 + - - +
73C ASP* 3.9 26.3 + - - +
101C ARG* 4.0 32.5 - - - +
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Residues in contact with LEU 579 (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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575B SER 2.9 17.9 + - - +
576B ILE* 3.8 3.1 - - - +
578B ARG* 1.3 76.7 - - - +
580B TRP* 1.3 62.0 + - - +
582B GLU* 4.8 1.8 - - + -
583B THR* 2.8 41.9 + - - +
589B LEU* 4.4 7.8 - - + +
593B ASP* 3.4 47.6 - - + +
620B TYR* 4.2 18.8 - - + -
97C THR* 4.0 14.6 - - + -
100C ASN* 4.2 8.5 - - + -
101C ARG* 3.8 31.6 - - + +
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Residues in contact with TRP 580 (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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563B ARG* 3.9 22.4 - - - -
564B GLY* 3.5 28.0 - - - -
565B ASP* 3.9 26.8 - - + +
576B ILE* 2.9 19.2 + - + +
577B LYS* 3.6 7.9 - - - +
579B LEU* 1.3 78.7 - - - +
581B THR* 1.3 74.9 + - + +
583B THR* 3.6 5.9 - - - +
586B LYS* 3.3 70.5 - - + +
589B LEU* 4.1 15.7 - - + -
593B ASP 5.5 2.0 - - - +
594B GLY 3.3 28.0 - - - -
595B GLY* 4.5 3.1 - - - -
596B PRO* 4.8 4.9 - - + -
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Residues in contact with THR 581 (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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577B LYS* 3.0 42.6 + - + +
578B ARG* 3.2 12.8 + - - -
580B TRP* 1.3 86.9 - - + +
582B GLU* 1.3 65.5 + - - +
583B THR 4.1 2.6 - - - +
586B LYS* 4.8 6.6 + - - +
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Residues in contact with GLU 582 (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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578B ARG* 3.0 52.2 + - - +
579B LEU* 4.5 2.2 - - + +
581B THR* 1.3 83.6 - - - +
583B THR* 1.3 66.3 + - - +
584B ILE* 3.8 8.5 + - - +
101C ARG* 4.6 26.5 + - + +
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Residues in contact with THR 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B LEU* 2.8 34.2 + - - +
580B TRP 3.6 13.2 - - - +
581B THR 4.1 1.2 - - - +
582B GLU* 1.3 79.4 - - - +
584B ILE* 1.3 61.2 - - - +
585B SER 5.1 2.0 - - - -
586B LYS* 3.8 12.1 + - - +
589B LEU* 4.1 14.9 - - + +
617B ASP* 3.3 34.5 - - + +
619B ASP* 5.2 6.3 - - - +
620B TYR* 4.2 17.3 - - + -
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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