Contacts of the helix formed by residues 622 - 641 (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 ASP 622 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619D ASP 3.4 8.7 + - - +
621D SER* 1.3 78.6 - - - +
623D GLU* 1.3 63.9 + - - +
624D GLN* 2.7 42.8 + - - +
625D THR* 2.8 47.4 + - + +
626D VAL* 3.7 5.5 + - - +
660D PHE* 4.0 2.2 - - - -
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Residues in contact with GLU 623 (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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621D SER 3.5 1.0 + - - -
622D ASP* 1.3 75.3 + - - +
624D GLN* 1.3 54.5 + - - +
626D VAL* 3.4 5.3 + - + +
627D THR* 2.7 44.4 + - - +
651D VAL* 4.1 23.7 - - + +
660D PHE* 3.5 34.5 - - + -
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Residues in contact with GLN 624 (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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622D ASP* 2.7 27.0 + - - +
623D GLU* 1.3 70.4 - - - +
625D THR* 1.3 59.5 + - + +
627D THR* 3.6 6.9 - - - -
628D ARG* 2.8 32.7 + - + +
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Residues in contact with THR 625 (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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619D ASP* 3.3 27.5 + - - +
622D ASP* 2.8 45.2 + - + +
624D GLN* 1.3 76.2 - - - +
626D VAL* 1.3 65.4 + - - +
628D ARG* 3.8 4.8 - - - +
629D TRP* 2.9 24.7 + - - +
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Residues in contact with VAL 626 (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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615D LEU* 6.0 4.3 - - + -
619D ASP* 3.6 28.7 - - + +
620D LEU* 4.9 1.8 - - + -
622D ASP 3.8 6.1 - - - +
623D GLU* 3.4 9.1 + - + +
624D GLN 3.4 0.2 - - - -
625D THR* 1.3 82.5 + - - +
627D THR* 1.3 59.6 + - - +
629D TRP* 3.3 8.9 + - + +
630D VAL* 2.9 31.3 + - + +
651D VAL* 5.3 13.2 - - + -
660D PHE* 4.5 21.5 - - + +
661D GLU 5.4 0.7 - - - -
662D PRO* 3.6 37.7 - - + -
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Residues in contact with THR 627 (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* 2.7 33.7 + - - +
624D GLN* 3.6 8.9 - - + -
625D THR 3.2 0.2 - - - -
626D VAL* 1.3 77.2 - - - +
628D ARG* 1.3 58.8 + - - +
630D VAL* 3.2 12.2 - - + +
631D ASN* 2.9 36.8 + - + +
649D PHE* 5.8 7.0 - - + -
651D VAL* 4.4 14.1 - - + +
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Residues in contact with ARG 628 (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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624D GLN* 2.8 22.0 + - + +
625D THR* 3.8 5.8 - - - +
627D THR* 1.3 76.1 - - - +
629D TRP* 1.3 64.7 + - - +
631D ASN* 3.3 10.5 + - - +
632D ALA* 2.9 55.5 + - - +
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Residues in contact with TRP 629 (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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605D MET* 6.5 0.9 - - - -
609D LEU* 4.2 22.7 - - + -
612D GLN* 4.7 8.7 + - + +
613D PRO* 4.0 34.7 + - + +
614D THR 4.1 10.7 + - - -
615D LEU* 3.6 43.5 - - + -
625D THR 2.9 18.1 + - - +
626D VAL* 3.6 9.0 - - + +
628D ARG* 1.3 78.3 - - - +
630D VAL* 1.3 68.7 + - + +
632D ALA* 3.3 5.7 + - + +
633D LEU* 3.0 42.2 + - + +
662D PRO* 3.9 31.6 - - + -
677D LEU* 3.9 16.6 - - + -
687D TYR* 4.8 4.0 - + - -
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Residues in contact with VAL 630 (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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626D VAL* 2.9 17.0 + - + +
627D THR* 3.2 22.0 - - + +
629D TRP* 1.3 86.5 - - + +
631D ASN* 1.3 59.3 + - + +
633D LEU* 3.6 9.0 - - + +
634D VAL* 2.9 40.7 + - + +
649D PHE* 3.7 37.5 - - + -
650D ASP 4.9 1.6 - - - +
651D VAL* 4.8 9.2 - - + -
662D PRO* 5.0 13.7 - - + -
663D ILE 4.7 8.3 - - - +
664D VAL* 4.9 11.0 - - + -
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Residues in contact with ASN 631 (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* 2.9 24.8 + - + +
628D ARG* 3.7 13.2 - - - +
630D VAL* 1.3 76.3 - - + +
632D ALA* 1.3 60.6 + - - +
634D VAL* 3.4 5.3 + - - +
635D SER* 2.9 33.8 + - - -
649D PHE* 5.6 13.0 - - + -
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Residues in contact with ALA 632 (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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612D GLN* 4.2 12.4 + - - +
613D PRO* 6.0 2.5 - - + -
628D ARG* 2.9 37.0 + - - +
629D TRP* 3.7 5.8 - - + +
631D ASN* 1.3 76.6 - - - +
633D LEU* 1.3 63.5 + - - +
635D SER* 3.8 4.4 - - - -
636D GLU* 3.0 26.2 + - - +
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Residues in contact with LEU 633 (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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605D MET* 4.6 19.3 - - + -
608D GLU* 3.8 17.3 - - + -
609D LEU* 4.8 8.1 - - + -
612D GLN* 3.7 32.7 + - + +
629D TRP* 3.0 38.5 + - + +
630D VAL* 3.6 11.2 - - + +
632D ALA* 1.3 78.4 - - - +
634D VAL* 1.3 57.2 + - + +
636D GLU* 3.3 1.6 + - - +
637D LEU* 2.9 47.8 + - + +
664D VAL* 4.5 21.5 - - + -
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Residues in contact with VAL 634 (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* 2.9 27.1 + - + +
631D ASN* 4.0 5.2 - - - +
633D LEU* 1.3 78.9 - - + +
635D SER* 1.3 58.9 + - - +
637D LEU* 3.3 8.3 + - + +
638D ASN* 2.9 35.7 + - - +
647D TRP* 3.4 33.7 - - + +
648D LYS* 4.0 13.7 - - - +
649D PHE* 3.8 28.9 - - + +
664D VAL* 5.2 8.1 - - + -
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Residues in contact with SER 635 (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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631D ASN* 2.9 25.2 + - - -
632D ALA* 3.8 4.7 - - - -
634D VAL* 1.3 77.4 - - - +
636D GLU* 1.3 56.7 + - - +
638D ASN* 3.3 7.5 + - - +
639D ASP* 2.9 29.2 + - - +
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Residues in contact with GLU 636 (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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608D GLU* 3.1 31.2 - - - +
612D GLN* 3.8 11.7 - - - +
632D ALA 3.0 16.9 + - - +
633D LEU 3.9 1.6 - - - +
635D SER* 1.3 76.9 - - - +
637D LEU* 1.3 57.5 + - - +
639D ASP* 3.3 15.5 + - - +
640D LYS* 2.9 53.2 + - + +
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Residues in contact with LEU 637 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604D ALA* 4.0 26.2 - - + +
605D MET* 4.6 7.2 - - + +
608D GLU* 4.0 26.9 - - + +
633D LEU* 2.9 43.6 + - + +
634D VAL* 3.7 7.2 - - + +
635D SER 3.2 0.2 - - - -
636D GLU* 1.3 77.3 - - - +
638D ASN* 1.3 56.5 + - - +
640D LYS* 3.3 5.6 + - + +
641D GLU* 2.9 30.8 + - - +
647D TRP* 3.6 45.0 + - + +
664D VAL* 5.3 4.0 - - + -
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Residues in contact with ASN 638 (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* 2.9 27.9 + - - +
635D SER* 3.9 6.3 - - - +
637D LEU* 1.3 75.0 - - - +
639D ASP* 1.3 63.0 + - - +
641D GLU* 3.6 16.3 + - - +
645D SER 5.1 0.3 - - - +
646D GLN* 3.5 7.7 - - - +
647D TRP* 2.9 51.1 + - - +
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Residues in contact with ASP 639 (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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635D SER* 2.9 19.3 + - - +
636D GLU* 3.5 22.6 - - - +
637D LEU 3.2 0.2 - - - -
638D ASN* 1.3 79.8 - - - +
640D LYS* 1.3 64.9 + - - +
641D GLU 3.3 5.4 + - - +
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Residues in contact with LYS 640 (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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608D GLU* 4.5 8.5 - - - +
636D GLU* 2.9 43.9 + - + +
637D LEU* 4.1 5.6 - - + +
639D ASP* 1.3 79.3 - - - +
641D GLU* 1.3 59.2 + - - +
642D GLN* 3.0 17.7 + - - +
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Residues in contact with GLU 641 (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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637D LEU 2.9 17.7 + - - +
638D ASN* 3.8 17.1 - - - +
639D ASP 3.2 4.8 - - - +
640D LYS* 1.3 72.9 - - - +
642D GLN* 1.3 58.1 + - - +
643D HIS* 3.1 41.4 - - - +
645D SER* 3.2 45.8 - - - +
647D TRP* 3.6 20.0 + - + +
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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