Contacts of the helix formed by residues 608 - 624 (chain B) in PDB entry 1GKU
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 ASN 608 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580B SER* 2.7 27.9 + - - -
581B ILE 3.2 4.3 - - - +
582B LYS* 3.2 33.4 + - - +
607B ASP* 1.3 73.0 + - - +
609B SER* 1.3 59.5 + - - +
610B ARG* 3.0 40.9 + - - +
611B SER* 2.7 31.9 + - - -
612B ARG* 3.9 1.6 + - - +
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Residues in contact with SER 609 (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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552B SER 5.2 2.6 + - - -
553B ILE 5.6 0.2 + - - -
555B HIS 3.6 14.7 + - - -
556B VAL* 2.9 34.5 + - - -
580B SER* 3.8 7.9 - - - -
581B ILE* 3.4 14.8 + - - +
608B ASN* 1.3 73.8 - - - +
610B ARG* 1.3 65.8 + - - +
611B SER 3.1 0.2 - - - -
612B ARG* 3.0 14.8 + - - +
613B ILE* 2.8 29.0 + - - +
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Residues in contact with ARG 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 5.7 8.7 - - + +
16B ALA* 6.3 2.9 - - - +
580B SER* 3.4 12.1 - - - +
608B ASN* 3.0 32.4 + - - +
609B SER* 1.3 77.1 - - - +
611B SER* 1.3 66.8 + - - +
613B ILE* 3.2 11.7 + - + +
614B GLU* 2.7 62.2 + - + +
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Residues in contact with SER 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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533B ASP* 3.5 18.7 - - - +
534B GLY* 4.3 14.8 + - - -
607B ASP* 5.6 0.7 - - - +
608B ASN* 2.7 26.2 + - - -
610B ARG* 1.3 78.4 - - - +
612B ARG* 1.3 61.3 + - - +
613B ILE 2.9 1.8 - - - -
614B GLU* 2.7 40.1 + - - +
615B ALA* 2.8 11.4 + - - +
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Residues in contact with ARG 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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514B PRO* 5.8 0.4 - - - +
534B GLY 2.7 35.4 + - - +
535B ALA* 3.5 23.7 - - - +
536B VAL* 4.3 11.1 + - - +
550B THR* 4.8 0.4 - - - +
551B ALA* 2.6 35.4 + - - +
552B SER* 4.0 17.8 - - - +
553B ILE* 3.5 32.3 - - + +
556B VAL* 5.8 2.0 - - + -
608B ASN 4.7 0.9 - - - +
609B SER* 3.0 22.2 + - - +
611B SER* 1.3 80.0 + - - +
613B ILE* 1.3 58.8 + - + +
615B ALA* 3.6 3.0 + - - +
616B LEU* 2.9 46.0 + - + +
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Residues in contact with ILE 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 5.7 2.7 - - + -
556B VAL* 3.6 32.3 - - + +
557B VAL* 5.7 1.3 - - + -
580B SER* 5.7 0.9 - - - -
609B SER* 2.8 29.7 + - - +
610B ARG* 3.3 11.7 - - + +
612B ARG* 1.3 76.7 - - + +
614B GLU* 1.3 60.6 + - + +
616B LEU* 3.9 11.8 - - + +
617B ARG* 2.9 56.7 + - - +
643B LEU* 5.0 1.6 - - + -
646B LEU* 3.4 35.9 - - + +
647B LEU* 4.7 3.1 - - + +
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Residues in contact with GLU 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ASP* 4.3 15.4 - - - +
610B ARG* 2.7 54.5 + - + +
611B SER* 2.7 26.9 + - - +
613B ILE* 1.3 71.4 - - + +
615B ALA* 1.3 61.2 + - - +
617B ARG* 3.3 13.3 + - - +
618B LYS* 3.1 23.5 + - - +
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Residues in contact with ALA 615 (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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532B LEU* 3.8 19.4 - - + +
533B ASP* 3.8 18.7 + - - +
534B GLY 4.6 1.1 - - - -
535B ALA* 3.7 26.2 - - + -
611B SER 2.8 10.0 + - - +
612B ARG 3.7 7.9 - - - +
614B GLU* 1.3 77.6 - - - +
616B LEU* 1.3 57.4 + - - +
618B LYS* 3.3 6.7 + - - +
619B LEU* 3.0 34.7 + - + +
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Residues in contact with LEU 616 (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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508B LEU* 4.0 8.5 - - + +
510B ILE* 3.5 33.0 - - + -
550B THR* 4.9 14.4 - - + -
551B ALA 5.3 1.6 - - - +
552B SER* 5.0 5.6 - - - -
556B VAL* 4.6 5.4 - - + -
612B ARG* 2.9 42.7 + - - +
613B ILE* 3.9 15.3 - - + +
614B GLU 3.3 0.2 - - - -
615B ALA* 1.3 72.6 - - + +
617B ARG* 1.3 60.7 + - - +
619B LEU* 3.7 9.7 - - + +
620B ALA* 2.9 31.0 + - - +
643B LEU* 3.9 26.9 - - + -
647B LEU* 3.8 12.9 - - + +
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Residues in contact with ARG 617 (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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14B ALA* 3.4 30.1 - - - +
15B ALA* 4.1 13.3 - - - +
34B LEU 5.4 7.2 - - - -
35B CYS* 4.5 5.6 - - - -
37B PHE* 4.5 9.6 - - + -
613B ILE* 2.9 43.7 + - - +
614B GLU* 3.5 11.5 - - - +
616B LEU* 1.3 77.8 - - - +
618B LYS* 1.3 57.4 + - - +
620B ALA* 3.3 4.1 + - - +
621B HIS* 2.9 29.7 + - - +
646B LEU* 3.2 37.7 + - - +
647B LEU* 3.8 9.6 - - + +
650B CYS* 4.0 16.5 - - - -
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Residues in contact with LYS 618 (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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37B PHE* 3.9 17.5 - - + -
70B ARG* 3.3 46.0 - - - +
72B GLU* 3.4 14.9 + - - +
532B LEU* 4.4 19.3 - - + +
533B ASP* 4.7 13.4 + - - -
614B GLU 3.1 12.4 + - - +
615B ALA* 3.6 9.2 - - - +
617B ARG* 1.3 77.0 - - - +
619B LEU* 1.3 58.7 + - + +
621B HIS* 3.3 2.6 + - - +
622B ASP* 3.0 30.5 + - - +
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Residues in contact with LEU 619 (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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67B ARG* 6.3 0.4 - - - +
508B LEU* 3.9 19.0 - - + +
530B LYS* 6.0 1.3 - - + -
532B LEU* 3.3 31.9 - - + -
535B ALA* 5.5 2.0 - - + -
537B VAL* 4.7 19.1 - - + -
548B MET* 4.4 22.1 - - - +
550B THR* 4.3 23.6 - - + +
615B ALA* 3.0 23.1 + - + +
616B LEU* 3.7 10.3 - - + +
618B LYS* 1.3 76.7 - - + +
620B ALA* 1.3 58.7 + - - +
622B ASP* 3.4 9.7 + - + +
623B ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 620 (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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508B LEU* 4.0 2.9 - - + +
616B LEU 2.9 18.2 + - - +
617B ARG 3.6 4.5 - - - +
619B LEU* 1.3 75.1 - - - +
621B HIS* 1.3 59.1 + - - +
623B ALA* 4.5 1.3 - - - +
624B GLU* 2.7 34.0 + - - -
625B PHE 4.2 0.3 + - - -
626B VAL* 3.7 29.1 - - + +
647B LEU* 4.2 13.0 - - + -
650B CYS* 3.8 22.4 - - + +
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Residues in contact with HIS 621 (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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35B CYS* 3.7 21.2 + - - -
37B PHE* 3.3 45.4 - + + -
40B ASP* 2.9 43.0 + - - -
66B LYS* 2.9 43.7 + - + +
70B ARG* 3.5 14.6 + - - -
617B ARG 2.9 18.2 + - - +
618B LYS 3.3 2.7 + - - +
620B ALA* 1.3 77.9 - - - +
622B ASP* 1.3 59.4 + - - +
624B GLU* 3.7 7.8 - - - +
650B CYS* 3.9 11.0 - - - +
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Residues in contact with ASP 622 (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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59B ALA 5.4 0.5 - - - +
63B MET* 3.5 37.5 + - + +
66B LYS* 3.3 26.0 - - - +
67B ARG* 3.6 18.4 + - - +
70B ARG* 2.7 39.5 + - - -
72B GLU* 5.1 0.5 - - - +
506B PRO* 4.8 1.2 - - - +
548B MET* 5.3 2.5 - - + -
618B LYS* 3.0 18.2 + - - +
619B LEU* 3.8 10.2 - - + +
621B HIS* 1.3 78.2 - - - +
623B ALA* 1.3 64.3 - - - +
624B GLU* 4.3 1.0 - - - +
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Residues in contact with ALA 623 (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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59B ALA* 6.1 0.3 - - - +
506B PRO* 4.0 24.3 - - - +
507B ALA 4.4 4.0 - - - +
508B LEU* 4.0 9.0 - - + +
548B MET* 3.5 19.9 - - + +
619B LEU 3.0 17.6 + - - +
620B ALA 4.1 1.6 - - - +
622B ASP* 1.3 77.0 - - - +
624B GLU* 1.3 68.5 + - - +
625B PHE* 2.9 28.0 + - - +
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Residues in contact with GLU 624 (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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43B LEU* 5.5 1.4 - - - +
62B LYS* 5.6 6.2 - - - +
66B LYS* 3.3 23.2 + - - +
620B ALA 2.7 20.5 + - - -
621B HIS 3.7 15.3 - - - +
622B ASP 4.3 2.7 - - - +
623B ALA* 1.3 76.2 - - - +
625B PHE* 1.3 58.6 + - - +
626B VAL* 5.4 0.7 - - - -
650B CYS 3.5 15.9 - - - +
651B GLY* 3.3 22.2 - - - -
652B ALA* 3.3 5.2 + - - +
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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