Contacts of the strand formed by residues 605 - 610 (chain A) in PDB entry 2VKX
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 LYS 605 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A ALA 4.0 0.8 + - - +
604A PRO* 1.3 76.1 - - - +
606A LEU* 1.3 64.6 + - - +
621A LEU* 3.9 0.9 - - - -
622A ILE* 3.0 62.8 + - + +
624A GLN* 4.0 18.1 - - - +
571B THR* 4.4 10.1 + - - -
594B LYS* 4.0 37.6 - - + +
641D LEU* 5.5 4.6 - - - +
670D GLU* 4.3 7.1 + - - -
686D HIS* 4.2 25.8 + - - -
688D VAL* 4.3 17.0 - - - +
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Residues in contact with LEU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A PRO* 3.9 5.6 + - + -
605A LYS* 1.3 79.3 - - - +
607A GLU* 1.3 62.0 + - - +
619A VAL* 4.2 13.7 - - + -
620A ASN 3.7 1.8 - - - -
621A LEU* 3.6 29.6 - - + -
622A ILE* 5.0 1.8 - - - -
671A VAL* 4.7 1.3 - - + +
673A VAL* 3.7 26.9 - - + -
685A ALA* 3.6 36.3 - - + +
686A HIS 4.1 2.9 - - - +
687A PHE* 3.7 37.3 - - + +
688D VAL* 3.8 19.8 + - - +
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Residues in contact with GLU 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LEU* 1.3 76.1 - - - +
608A GLY* 1.3 65.4 + - - +
618A LYS 3.7 0.2 - - - +
619A VAL* 3.6 3.6 - - - -
620A ASN* 2.8 67.5 + - + +
622A ILE* 4.4 8.7 - - + +
687A PHE* 4.7 0.9 - - - -
592B GLU* 4.3 4.6 - - - +
668D GLU* 2.5 39.9 - - - +
688D VAL* 3.3 24.5 - - + +
689D PHE* 3.7 18.8 - - - -
690D ARG* 3.3 18.4 + - - +
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Residues in contact with GLY 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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607A GLU* 1.3 74.3 - - - +
609A GLN* 1.3 59.8 + - - +
617A ILE* 4.3 3.8 - - - -
618A LYS 3.6 4.7 - - - -
619A VAL* 4.8 1.1 - - - -
687A PHE* 3.6 29.8 - - - -
688D VAL 3.1 10.1 + - - -
689D PHE* 3.1 9.4 - - - +
690D ARG 2.9 25.3 + - - -
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Residues in contact with GLN 609 (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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608A GLY* 1.3 74.7 - - - +
610A ARG* 1.3 74.3 + - + +
617A ILE* 3.2 9.4 - - - +
618A LYS* 2.9 56.3 + - + +
620A ASN* 3.0 28.3 + - - +
690D ARG* 3.2 45.8 + - + +
691D THR 4.6 5.0 + - - +
692D ALA* 5.3 1.7 - - - +
1696D SO4 4.4 17.6 + - - -
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Residues in contact with ARG 610 (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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609A GLN* 1.3 95.8 + - + +
611A GLY* 1.3 66.7 + - - +
616A SER 5.2 0.9 - - - -
617A ILE* 5.4 0.4 - - - +
618A LYS* 4.0 6.3 - - - +
610D ARG* 3.4 57.5 - - + +
611D GLY 3.7 20.6 + - - -
612D GLU 4.2 5.7 + - - -
613D ASP* 3.7 14.9 + - - +
614D GLY* 3.3 32.7 - - - +
616D SER 5.6 3.3 + - - +
690D ARG 4.3 3.3 + - - +
692D ALA* 4.5 18.4 - - + +
1696D SO4 5.1 7.1 + - - +
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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