Contacts of the helix formed by residues 607 - 612 (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 PRO 607 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B SER* 5.5 8.7 - - - +
527B THR* 6.1 0.2 - - - +
599B TYR* 4.0 2.7 - - - +
605B HIS 3.8 7.2 - - - +
606B ILE* 1.3 89.1 - - + +
608B GLU* 1.3 65.4 + - - +
609B VAL* 3.3 1.1 - - + +
610B CYS* 3.3 35.4 + - - -
611B LEU* 3.4 8.3 + - - +
658B ASP 3.5 24.7 - - - +
659B ALA* 4.4 10.5 - - + -
660B VAL* 4.3 11.7 - - + -
118C TYR* 4.0 20.0 - - + -
121C ARG* 4.2 5.4 - - - +
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Residues in contact with GLU 608 (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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523B MET* 3.4 36.7 - - + +
555B TYR* 5.4 0.2 + - - -
590B LEU* 3.7 18.6 - - + +
591B VAL* 3.1 39.1 + - - +
592B ALA 5.6 0.3 + - - -
598B PRO* 4.2 12.7 - - + +
599B TYR* 3.4 24.6 + - + +
607B PRO* 1.3 76.3 - - - +
609B VAL* 1.3 66.0 + - + +
611B LEU* 3.4 12.9 + - - +
612B LYS* 3.5 24.9 + - - +
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Residues in contact with VAL 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B SER* 5.1 9.0 - - - +
590B LEU* 4.5 18.6 - - + -
607B PRO* 3.3 0.8 - - + -
608B GLU* 1.3 79.1 - - + +
610B CYS* 1.3 61.6 + - - +
612B LYS 3.8 0.5 + - - -
613B TRP* 3.6 41.9 + - + -
616B MET* 3.9 11.5 - - + +
624B LEU* 5.1 2.0 - - + -
625B CYS* 4.6 3.8 - - - -
660B VAL* 3.7 37.0 - - + +
662B THR* 4.3 30.5 - - + +
119C PHE* 5.3 0.9 - - + -
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Residues in contact with CYS 610 (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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606B ILE* 4.1 9.0 - - + -
607B PRO* 3.3 30.7 - - - +
608B GLU 3.2 0.2 - - - -
609B VAL* 1.3 76.4 - - - +
611B LEU* 1.3 61.9 + - - +
612B LYS 3.3 0.6 + - - -
613B TRP* 3.6 9.7 + - - +
660B VAL* 4.0 11.7 - - - -
118C TYR* 3.5 34.8 - - + +
119C PHE* 4.0 28.4 - - + -
122C LEU* 3.3 22.2 - - + +
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Residues in contact with LEU 611 (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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598B PRO* 3.7 33.7 - - + +
599B TYR* 4.4 15.3 - - + -
603B ASN* 3.4 33.7 - - + +
606B ILE* 4.2 17.0 - - + +
607B PRO 3.4 10.4 + - - +
608B GLU* 3.9 8.7 - - - +
609B VAL 3.4 0.4 - - - -
610B CYS* 1.3 80.3 - - - +
612B LYS* 1.3 59.5 + - + +
613B TRP 3.5 0.6 + - - -
614B SER* 5.5 2.6 + - - -
615B LEU* 5.3 4.5 - - - +
122C LEU* 4.1 23.1 - - + +
125C LEU* 5.4 2.7 - - + -
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Residues in contact with LYS 612 (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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587B ALA 4.0 14.8 - - - +
588B GLY* 3.6 19.5 - - - +
589B LEU 2.5 32.4 + - - +
590B LEU* 3.6 9.9 - - + +
591B VAL 4.1 0.2 - - - +
596B PRO* 2.8 27.1 + - - -
598B PRO* 3.7 22.8 - - + +
608B GLU* 3.5 35.8 + - - +
609B VAL 3.8 0.4 + - - -
610B CYS 3.3 0.6 - - - -
611B LEU* 1.3 84.9 - - + +
613B TRP* 1.3 61.3 + - - -
614B SER 3.5 2.0 - - - -
615B LEU* 3.4 13.1 + - + -
616B MET* 3.3 32.1 + - + +
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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