Contacts of the strand formed by residues 646 - 653 (chain D) in PDB entry 6RKU
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 GLN 646 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638D ASN* 3.7 8.5 - - - +
645D SER* 1.3 87.9 + - - +
647D TRP* 1.3 79.1 + - - +
648D LYS* 4.3 19.7 + - + -
666D VAL* 3.3 12.5 - - - +
667D ARG* 3.5 36.2 + - + +
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Residues in contact with TRP 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D PRO* 5.0 13.7 - - + -
604D ALA* 3.6 31.1 - - + +
605D MET* 5.0 7.4 - - + -
634D VAL* 3.4 14.4 - - + +
637D LEU* 3.6 46.3 + - + +
638D ASN* 2.9 39.1 + - - +
641D GLU* 3.6 23.5 + - + -
645D SER* 4.6 1.9 + - - -
646D GLN* 1.3 93.9 + - - +
648D LYS* 1.3 68.1 + - - +
664D VAL* 3.8 26.5 - - + -
665D ARG 3.8 4.5 - - - -
666D VAL* 3.5 35.4 - - + -
675D TYR* 6.1 1.6 - + - -
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Residues in contact with LYS 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634D VAL* 4.1 8.5 - - - +
646D GLN* 4.3 18.7 + - + +
647D TRP* 1.3 81.4 - - - +
649D PHE* 1.3 62.4 + - + +
664D VAL* 3.6 7.1 - - - +
665D ARG* 2.6 65.4 + - + +
667D ARG* 5.1 19.4 - - + +
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Residues in contact with PHE 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627D THR* 5.8 7.2 - - + -
630D VAL* 3.7 35.7 - - + +
631D ASN* 5.6 11.9 - - + -
634D VAL* 3.8 17.5 - - + -
648D LYS* 1.3 83.3 - - + +
650D ASP* 1.3 72.4 + - - +
651D VAL* 4.7 9.0 - - + -
663D ILE 3.6 4.9 - - - -
664D VAL* 4.8 0.2 - - - +
665D ARG* 4.6 5.5 + - - +
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Residues in contact with ASP 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630D VAL* 4.9 3.0 - - - +
649D PHE* 1.3 82.5 - - - +
651D VAL* 1.3 76.5 + - - +
652D HIS* 4.1 4.2 - - - +
662D PRO* 3.9 2.6 - - - +
663D ILE* 2.8 72.8 + - + +
665D ARG* 4.7 20.4 + - + +
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Residues in contact with VAL 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623D GLU* 4.1 28.0 - - + +
626D VAL* 5.3 12.8 - - + -
627D THR* 4.4 18.2 - - + +
630D VAL* 4.8 11.4 - - + -
649D PHE* 4.7 15.4 - - + -
650D ASP* 1.3 83.5 + - - +
652D HIS* 1.3 69.5 + - - +
653D THR* 5.3 6.3 - - + -
660D PHE* 5.7 5.8 - - + -
661D GLU 4.7 2.7 - - - +
662D PRO* 5.3 1.6 - - + -
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Residues in contact with HIS 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650D ASP* 4.1 4.0 - - - +
651D VAL* 1.3 78.1 - - - +
653D THR* 1.3 96.1 + - - +
654D ASN* 3.5 27.0 + - + +
660D PHE* 4.1 2.4 - - - -
661D GLU* 3.4 36.4 + - + +
663D ILE* 3.7 27.8 - - + +
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Residues in contact with THR 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623D GLU* 6.1 1.3 - - - +
651D VAL* 5.3 6.3 - - + -
652D HIS* 1.3 92.1 + - - +
654D ASN* 1.3 58.4 + - - +
655D ALA 3.8 2.6 + - - -
657D GLN 4.9 6.5 - - - +
658D ASN 3.8 12.6 - - - -
660D PHE* 3.4 30.5 - - + -
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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