Contacts of the helix formed by residues 599 - 619 (chain B) in PDB entry 5SY1
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 599 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ASN* 1.3 75.8 - - - +
600B VAL* 1.3 62.5 + - + +
602B ASN* 3.3 14.1 + - + +
603B ALA* 3.1 23.9 + - - +
124D GLU* 5.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ASN* 3.1 19.4 + - + +
599B LYS* 1.3 80.2 - - + +
601B SER* 1.3 63.4 + - - +
603B ALA* 3.1 17.9 + - + +
604B LYS* 3.3 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ASN* 2.6 44.4 + - - -
600B VAL* 1.3 70.7 - - - +
602B ASN* 1.3 59.5 + - - +
604B LYS* 3.2 13.2 + - - +
605B ARG* 2.8 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ASN 2.9 19.2 + - - +
599B LYS* 3.4 15.7 - - - +
600B VAL 3.2 0.4 - - - -
601B SER* 1.3 76.0 + - - +
603B ALA* 1.3 53.9 + - - +
605B ARG* 3.3 29.0 + - - +
606B ALA* 2.4 35.8 + - - +
121D GLU* 3.2 28.2 + - - +
124D GLU* 4.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B LYS 3.1 12.4 + - - +
600B VAL* 3.1 13.7 + - + +
602B ASN* 1.3 74.9 - - - +
604B LYS* 1.3 58.7 + - - +
606B ALA* 3.9 8.3 - - - -
607B ARG* 2.9 22.5 + - - +
128D GLU* 3.1 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B VAL 3.3 4.8 + - - +
601B SER* 3.2 19.4 + - - +
603B ALA* 1.3 78.4 - - - +
605B ARG* 1.3 56.3 - - + +
607B ARG* 3.3 23.9 + - - +
608B ALA* 2.8 26.7 + - + +
55D GLU* 5.7 7.6 - - - -
75D ARG* 5.3 15.9 - - - +
148D SER 4.2 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ASN 3.1 27.5 + - - +
601B SER* 2.8 34.8 + - - +
602B ASN* 3.3 36.1 + - - +
604B LYS* 1.3 70.9 - - + +
606B ALA* 1.3 56.1 + - - +
608B ALA* 3.4 9.7 - - + +
609B HIS* 2.7 49.7 + - + +
57D ASP 6.1 1.3 - - - +
58D ALA* 5.2 12.3 - - - +
121D GLU* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B ASN* 2.4 21.0 + - - +
603B ALA* 3.2 6.0 + - - +
605B ARG* 1.3 71.2 - - - +
607B ARG* 1.3 60.7 + - - +
609B HIS* 3.9 6.4 + - - +
610B TRP* 3.3 31.5 + - - -
124D GLU 4.1 7.9 - - - +
125D MET* 4.0 30.1 - - + +
128D GLU* 3.3 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B ALA 2.9 12.9 + - - +
604B LYS* 3.5 29.3 - - - +
605B ARG 3.2 0.2 - - - -
606B ALA* 1.3 77.9 - - - +
608B ALA* 1.3 57.5 + - - +
610B TRP* 3.3 8.4 + - - +
611B GLN* 2.9 40.6 + - + +
75D ARG* 6.2 0.2 - - - +
128D GLU* 3.4 12.4 + - - +
144D THR 4.2 3.6 + - - -
145D MET* 3.6 57.0 + - + +
148D SER* 2.7 58.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B LYS* 2.8 18.3 + - + +
605B ARG* 3.0 12.7 + - + +
607B ARG* 1.3 77.5 - - - +
609B HIS* 1.3 57.6 + - - +
611B GLN* 3.4 3.5 + - - +
612B LEU* 3.1 31.5 + - - +
55D GLU 6.0 2.0 - - - +
58D ALA* 4.2 18.1 - - + +
75D ARG* 4.2 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ARG* 2.7 32.1 + - + +
606B ALA* 4.3 4.8 - - - +
607B ARG 3.3 0.2 - - - -
608B ALA* 1.3 73.4 - - + +
610B TRP* 1.3 62.8 + - - +
612B LEU* 3.6 14.2 + - + +
613B LEU* 3.4 24.7 + - - +
58D ALA* 3.1 38.2 + - + -
59D ASP* 5.0 1.6 - - - -
117D LEU* 3.5 36.2 - - + +
121D GLU* 4.0 25.8 + - + +
125D MET* 3.7 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B ALA 3.3 13.8 + - - -
607B ARG* 3.3 7.5 + - - +
608B ALA 3.2 0.6 - - - -
609B HIS* 1.3 77.9 - - - +
611B GLN* 1.3 59.4 + - - +
613B LEU* 2.9 18.2 + - + +
614B TYR* 2.8 28.3 + - - +
106D LEU* 4.7 8.9 - - + +
125D MET* 3.0 68.9 - - + +
126D ILE* 3.9 13.5 - - + -
128D GLU* 4.4 4.0 - - - -
129D ALA* 3.7 25.4 - - + -
137D VAL* 5.7 2.7 - - + -
141D GLU 5.2 2.2 - - - -
142D PHE* 5.4 16.9 - + + -
145D MET* 3.5 41.3 - - + -
146D MET* 4.5 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ARG* 2.9 33.1 + - + +
608B ALA* 3.4 5.0 + - - +
609B HIS 3.4 0.2 - - - -
610B TRP* 1.3 73.8 - - - +
612B LEU* 1.3 64.3 + - - +
614B TYR* 3.8 8.5 - - + +
615B THR* 3.1 26.9 + - - -
2D ALA* 5.6 0.7 - - - +
71D THR* 3.8 10.8 - - + +
75D ARG* 2.5 53.6 + - - +
145D MET 3.6 18.0 + - - -
146D MET* 4.2 25.0 + - + +
148D SER 4.7 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ALA 3.1 15.5 + - - +
609B HIS* 3.6 17.9 - - + +
610B TRP 3.2 0.2 - - - -
611B GLN* 1.3 78.7 - - - +
613B LEU* 1.3 65.1 + - + +
615B THR* 3.6 2.1 + - - -
616B LEU* 3.3 33.1 + - + +
626B ARG* 4.5 28.5 - - - +
58D ALA* 3.7 29.8 - - + -
59D ASP* 5.1 2.2 - - - +
67D PRO* 4.4 19.3 - - + +
68D GLU* 4.3 24.9 - - + +
71D THR* 4.7 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B HIS 3.4 15.5 + - - +
610B TRP* 2.9 19.5 + - + +
612B LEU* 1.3 79.5 - - + +
614B TYR* 1.3 59.5 + - - +
616B LEU* 3.2 8.7 + - + +
617B VAL* 3.0 36.9 + - + +
93D PHE* 4.6 17.3 - - + -
106D LEU* 4.4 22.9 - - + -
109D VAL* 5.1 7.0 - - + -
110D MET* 4.7 22.9 - - + -
113D LEU* 4.7 20.6 - - + +
125D MET* 5.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B TRP 2.8 14.3 + - - +
611B GLN* 4.1 6.3 - - + +
612B LEU 3.4 0.4 - - - -
613B LEU* 1.3 76.5 - - - +
615B THR* 1.3 61.1 + - - +
617B VAL* 4.4 4.3 - - + +
618B ASN* 3.6 30.4 + - - -
2D ALA* 3.2 50.8 - - + +
3D ASP* 2.4 24.9 + - - -
78D LYS* 5.1 7.2 + - - -
85D GLU* 4.5 2.6 - - - +
86D ILE* 3.7 27.4 + - + +
89D ALA* 4.0 20.2 - - + -
93D PHE* 4.9 5.1 - + - -
142D PHE* 3.8 26.9 - + + -
146D MET* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B GLN 3.1 17.2 + - - -
612B LEU* 3.9 4.3 - - - -
613B LEU 3.2 0.6 - - - -
614B TYR* 1.3 78.9 - - - +
616B LEU* 1.3 60.1 + - + +
618B ASN* 3.3 2.6 + - - -
619B ASN* 3.0 46.9 + - + +
622B LEU* 5.0 4.0 - - + -
2D ALA* 3.9 24.6 - - - +
67D PRO* 5.3 8.1 - - + -
70D LEU* 3.9 22.9 - - + -
71D THR* 3.3 20.8 - - + +
74D ALA* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B LEU* 3.3 23.1 + - + +
613B LEU* 3.2 10.8 + - + +
615B THR* 1.3 75.8 - - + +
617B VAL* 1.3 64.8 + - - +
619B ASN* 3.0 18.6 - - - +
620B PRO* 4.0 2.3 - - - +
622B LEU* 4.3 15.7 - - + +
623B VAL* 3.8 40.7 - - + +
626B ARG* 3.7 35.2 - - - +
67D PRO* 4.7 11.7 - - + -
113D LEU* 4.1 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LEU 3.0 21.0 + - - +
614B TYR* 4.4 4.3 - - + +
616B LEU* 1.3 80.1 - - - +
618B ASN* 1.3 70.4 + - - +
619B ASN 3.2 1.4 + - - -
620B PRO* 4.3 10.7 - - - +
89D ALA* 5.3 6.3 - - + +
92D VAL* 4.3 32.1 - - + -
93D PHE* 3.9 28.5 - - + -
109D VAL* 4.3 18.8 - - + -
113D LEU* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B TYR* 3.6 47.7 + - - +
615B THR 3.3 3.7 + - - +
617B VAL* 1.3 86.4 - - - +
619B ASN* 1.3 66.5 + - - +
620B PRO* 3.9 7.1 - - - +
2D ALA 3.8 2.8 + - - +
3D ASP* 3.8 9.4 + - - +
4D GLN* 3.6 39.3 - - + +
85D GLU* 5.1 7.4 + - - +
88D GLU* 5.6 5.2 - - - +
89D ALA* 5.0 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B THR* 3.0 34.9 + - - +
616B LEU* 3.0 17.2 - - - +
617B VAL 3.2 0.4 - - - -
618B ASN* 1.3 85.1 - - - +
620B PRO* 1.3 67.6 - - - +
621B SER* 3.5 2.7 - - - +
622B LEU* 3.7 32.3 + - + +
623B VAL* 4.1 1.7 - - - +
2D ALA* 5.0 1.0 - - - +
3D ASP 3.3 17.6 + - - -
4D GLN* 4.8 0.3 - - - +
5D LEU* 3.5 24.1 + - - +
10D ILE* 4.1 13.1 - - + +
70D LEU* 4.5 6.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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