Contacts of the helix formed by residues 603 - 613 (chain I) in PDB entry 2VKZ
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 SER 603 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599I PRO 5.3 0.7 - - - -
600I CYS 4.3 8.7 - - - -
601I THR 3.2 2.9 - - - +
602I VAL* 1.3 84.6 - - - +
604I PRO* 1.3 67.9 - - - +
605I ASP* 3.2 23.0 + - - +
606I PHE* 3.2 13.6 + - - +
607I VAL* 2.9 18.3 + - - +
812I LYS* 3.6 31.7 - - - +
1038I GLU* 5.4 0.2 - - - -
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Residues in contact with PRO 604 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602I VAL 3.4 8.9 - - - +
603I SER* 1.3 85.8 - - - +
605I ASP* 1.3 63.3 + - - +
607I VAL* 3.3 11.6 - - + +
608I ALA* 2.9 31.7 + - - +
619I LEU* 5.1 0.7 - - + -
624I TYR* 3.9 8.3 - - - +
633I ALA* 4.0 11.0 - - + +
636I SER* 3.4 31.4 - - - +
637I VAL* 3.5 17.9 - - + +
640I GLN* 3.9 2.8 + - - -
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Residues in contact with ASP 605 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603I SER* 3.4 10.3 + - - +
604I PRO* 1.3 85.4 - - - +
606I PHE* 1.3 59.7 + - - +
608I ALA* 3.3 2.6 - - - +
609I ALA* 2.8 29.3 + - - +
636I SER* 4.8 0.3 + - - -
640I GLN* 3.1 29.9 + - - +
810I GLU* 5.1 0.9 - - - +
812I LYS* 3.7 27.9 + - - +
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Residues in contact with PHE 606 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594I VAL* 4.0 9.9 - - + -
600I CYS* 3.7 25.4 - - + +
601I THR* 4.5 6.5 - - - -
603I SER* 3.2 14.1 + - - +
605I ASP* 1.3 76.7 - - - +
607I VAL* 1.3 60.3 + - - +
609I ALA* 4.3 3.8 - - - -
610I THR* 2.9 51.4 + - - -
617I ILE* 3.6 21.8 - - + -
805I VAL* 3.1 28.3 - - + -
808I ALA* 4.4 1.6 - - + -
810I GLU* 3.4 32.4 + - + +
811I VAL* 3.2 31.0 - - + -
1070I ILE* 3.7 17.0 - - + -
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Residues in contact with VAL 607 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601I THR* 4.2 6.1 - - + +
603I SER 2.9 21.1 + - - +
604I PRO* 3.3 20.6 - - + +
606I PHE* 1.3 73.1 - - - +
608I ALA* 1.3 65.0 + - - +
611I THR* 3.0 24.1 + - - -
617I ILE* 3.4 32.3 - - + +
619I LEU* 3.9 22.2 - - + +
637I VAL* 3.5 24.7 - - + -
647I PHE* 4.3 17.3 - - + -
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Residues in contact with ALA 608 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604I PRO 2.9 19.9 + - - +
605I ASP 3.3 3.8 - - - +
607I VAL* 1.3 75.5 - - - +
609I ALA* 1.3 57.6 + - - +
611I THR* 2.9 9.6 + - - +
612I ASN* 2.7 43.6 + - - +
637I VAL* 4.3 11.9 - - - +
640I GLN* 3.6 35.4 - - + +
641I ILE 5.2 0.9 - - - +
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Residues in contact with ALA 609 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605I ASP 2.8 18.9 + - - +
606I PHE* 4.0 3.8 - - - +
608I ALA* 1.3 72.6 - - - +
610I THR* 1.3 57.4 + - - +
612I ASN* 3.3 7.5 + - - +
613I ALA* 2.9 29.5 + - - +
810I GLU* 4.1 33.7 - - + +
1070I ILE* 4.3 2.9 - - - +
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Residues in contact with THR 610 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594I VAL* 3.3 32.3 - - + -
606I PHE* 2.9 45.9 + - - -
609I ALA* 1.3 76.7 - - - +
611I THR* 1.3 61.4 + - - +
613I ALA* 3.5 7.6 + - - +
615I TYR* 3.2 28.2 + - + +
617I ILE* 3.8 17.3 - - + -
1070I ILE* 3.6 22.1 - - + +
1074I MET* 5.0 0.2 - - + -
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Residues in contact with THR 611 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589I ARG* 3.7 8.2 + - - +
607I VAL* 3.0 17.1 + - + +
608I ALA* 2.9 9.4 + - - +
610I THR* 1.3 77.3 - - - +
612I ASN* 1.3 62.8 + - - +
614I GLY* 3.0 19.6 + - - -
615I TYR 3.1 17.8 + - - +
617I ILE* 4.0 11.1 + - - +
637I VAL* 5.8 0.2 - - + -
641I ILE* 3.2 42.2 - - + -
645I SER* 5.0 3.3 - - - -
646I THR 3.1 18.9 + - - +
647I PHE* 4.1 5.1 - - + +
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Residues in contact with ASN 612 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608I ALA* 2.7 23.2 + - - +
609I ALA* 3.6 8.4 + - - +
611I THR* 1.3 74.1 + - - +
613I ALA* 1.3 55.4 - - - +
614I GLY* 2.8 11.3 + - - -
640I GLN* 2.9 22.1 + - - +
641I ILE* 3.4 9.4 - - - +
642I GLU* 3.3 38.0 + - - +
645I SER* 4.9 1.2 + - - -
1071I LYS* 5.6 0.5 + - - -
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Residues in contact with ALA 613 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609I ALA 2.9 16.5 + - - +
610I THR* 3.7 8.1 - - + +
611I THR 3.3 0.4 - - - -
612I ASN* 1.3 74.8 - - - +
614I GLY* 1.3 56.1 + - - +
615I TYR* 3.0 24.3 - - + -
1070I ILE* 4.4 4.0 - - + -
1071I LYS* 3.5 59.4 + - + +
1074I MET* 6.0 0.2 - - + -
1075I ASP* 4.7 0.2 - - - +
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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
------------------------------------------------------------
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