Contacts of the helix formed by residues 608 - 622 (chain J) in PDB entry 4E2I
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 SER 608 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581J TRP* 3.8 4.1 - - - -
604J ASP* 4.5 6.5 - - - -
607J PHE* 1.3 78.0 - - - +
609J LEU* 1.3 72.1 + - - +
610J SER* 2.9 27.8 + - - -
611J VAL* 3.7 12.5 - - - +
612J TYR* 3.6 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581J TRP* 4.6 21.8 - - + +
604J ASP* 4.4 15.5 - - - +
608J SER* 1.3 81.0 - - - +
610J SER* 1.3 63.5 + - - +
612J TYR* 4.0 1.3 - - - -
613J GLN* 2.7 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 610 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608J SER* 2.9 15.9 + - - -
609J LEU* 1.3 75.8 - - - +
611J VAL* 1.3 73.0 + - - +
612J TYR 3.1 1.6 - - - -
613J GLN* 3.5 3.4 + - - +
614J LYS* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385J GLU* 5.9 0.9 - - - +
606J GLU 5.5 1.8 - - - +
607J PHE* 3.5 33.2 - - + -
608J SER* 3.7 22.8 + - - +
609J LEU 3.6 0.2 - - - -
610J SER* 1.3 86.5 + - - +
612J TYR* 1.3 61.6 + - - +
614J LYS* 3.6 8.3 - - + +
615J MET* 3.2 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 612 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388J MET* 4.0 19.1 - - + -
391J VAL* 3.3 27.1 + - + +
392J ALA* 4.7 4.5 - - + -
581J TRP* 3.4 51.6 - + + -
582J TYR* 2.8 42.6 + + - -
607J PHE* 5.0 0.8 - - + -
608J SER 3.6 10.0 + - - +
609J LEU* 3.9 1.1 - - + +
610J SER 3.1 0.4 - - - -
611J VAL* 1.3 75.7 - - - +
613J GLN* 1.3 84.9 + - - +
614J LYS 3.0 3.8 - - - -
615J MET* 2.8 46.2 + - + +
616J LYS* 3.4 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 613 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582J TYR* 5.1 1.0 + - - -
609J LEU* 2.7 43.0 + - - +
610J SER* 4.3 2.5 - - - +
612J TYR* 1.3 98.9 - - - +
614J LYS* 1.3 57.2 + - - +
615J MET 3.1 0.2 - - - -
616J LYS* 3.3 20.7 + - + +
617J PHE* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 614 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610J SER 3.0 20.8 + - - +
611J VAL* 3.6 12.8 - - + +
612J TYR 3.0 0.4 - - - -
613J GLN* 1.3 77.5 - - - +
615J MET* 1.3 60.5 + - + +
617J PHE* 3.3 39.6 - - + +
618J ASN* 2.8 23.5 + - - -
627J ASP* 4.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 615 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385J GLU 4.4 2.0 - - - +
388J MET* 3.8 20.9 - - + +
389J ALA* 3.7 14.4 - - - -
392J ALA* 4.1 9.9 - - + -
607J PHE* 4.2 16.4 - - + -
611J VAL* 3.2 13.5 - - + +
612J TYR* 2.8 48.4 + - + +
614J LYS* 1.3 76.4 - - + +
616J LYS* 1.3 62.3 + - - +
617J PHE 3.0 5.5 + - - -
618J ASN* 3.2 11.4 + - - +
619J VAL* 3.1 17.5 + - - +
625J VAL* 3.2 25.6 - - + +
626J LEU* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392J ALA* 3.5 19.7 - - + -
395J HIS* 2.9 45.5 + - - -
396J CYS* 4.1 17.9 - - - -
582J TYR* 3.3 13.9 + - - +
612J TYR* 3.8 32.1 - - + +
613J GLN* 3.3 20.8 + - + +
615J MET* 1.3 75.7 - - - +
617J PHE* 1.3 62.1 + - - +
619J VAL* 3.1 25.2 - - - +
620J ALA* 3.2 8.5 + - - +
14U ILE 4.7 6.1 + - - -
15U PHE* 5.1 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 617 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613J GLN 2.9 14.0 + - - +
614J LYS* 3.3 34.1 - - + +
616J LYS* 1.3 73.2 - - - +
618J ASN* 1.3 75.5 + - - +
619J VAL 3.0 1.3 - - - -
620J ALA* 2.9 25.2 + - + +
621J MET* 3.1 51.1 + - + +
623J ILE* 5.5 1.1 - - + -
46U ILE* 5.5 2.7 - - + -
49U CYS* 5.4 3.4 - - + -
50U THR* 3.6 24.9 - - + -
55U VAL* 6.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 618 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614J LYS* 2.8 23.8 + - - +
615J MET* 3.2 5.0 + - - +
617J PHE* 1.3 87.8 - - - +
619J VAL* 1.3 57.5 + - - +
621J MET* 3.2 4.1 + - - +
622J GLY 2.8 25.1 + - - -
623J ILE* 3.0 40.3 + - + +
624J GLY 3.1 23.4 + - - +
625J VAL* 3.2 19.0 + - - -
627J ASP* 3.3 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 619 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393J TRP* 4.3 10.5 - - + +
396J CYS* 3.6 32.5 - - + -
552J TYR* 3.1 41.4 - - + +
553J LEU* 4.1 8.1 - - + -
556J CYS* 4.0 16.4 - - + -
615J MET 3.1 17.7 - - - +
616J LYS* 3.1 16.8 - - - +
617J PHE 3.0 0.2 - - - -
618J ASN* 1.3 79.6 - - - +
620J ALA* 1.3 62.3 + - - +
621J MET 3.3 0.3 + - - -
622J GLY 3.5 1.4 + - - -
625J VAL* 3.5 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552J TYR* 3.8 11.1 - - - +
616J LYS 3.2 7.2 + - - +
617J PHE* 2.9 13.4 + - + +
619J VAL* 1.3 80.1 - - - +
621J MET* 1.3 78.2 + - + +
15U PHE* 4.3 29.7 - - + -
43U GLY* 5.1 8.5 - - - +
46U ILE* 4.2 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 621 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552J TYR* 4.8 2.8 - - - +
555J HIS* 5.5 2.1 - - - -
617J PHE* 3.1 47.5 + - + +
618J ASN* 3.4 13.5 - - - +
619J VAL 3.2 0.2 - - - -
620J ALA* 1.3 95.7 - - + +
622J GLY* 1.3 57.4 + - - +
623J ILE* 3.7 20.2 - - + -
46U ILE* 3.7 23.6 - - + +
47U ALA* 5.1 5.8 - - - +
50U THR* 3.1 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 622 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552J TYR* 3.9 15.7 - - - -
555J HIS* 2.9 33.1 - - - +
559J ARG* 2.8 29.6 + - - -
618J ASN 2.8 7.3 + - - -
619J VAL 3.5 1.6 + - - -
621J MET* 1.3 76.6 - - - +
623J ILE* 1.3 58.3 + - - +
----------------------------------------------------------
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