Contacts of the helix formed by residues 608 - 625 (chain C) in PDB entry 1IW1
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 LEU 608 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C ALA 3.6 0.8 + - - -
607C GLY* 1.3 70.7 - - - -
609C ALA* 1.3 57.7 + - - +
611C GLU 3.3 0.5 + - - -
612C LEU* 2.9 43.0 + - + +
780C LEU* 3.3 41.3 - - + +
781C ASN* 3.1 6.2 + - - +
783C LEU* 4.8 3.4 - - + +
785C LEU* 3.7 24.9 - - + -
790C ARG* 3.7 37.7 - - + +
793C LEU* 4.1 19.1 - - + -
794C LEU* 4.1 22.2 - - + -
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Residues in contact with ALA 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C LEU* 1.3 77.3 - - - +
610C VAL* 1.3 63.4 + - + +
612C LEU* 3.5 3.0 + - - +
613C LYS* 3.1 23.9 + - - +
730C TYR* 4.8 1.4 + - + -
777C ARG* 3.5 42.3 - - + +
780C LEU* 4.1 16.7 - - + +
781C ASN* 3.0 18.8 + - - +
903C HEM 4.5 4.8 - - - +
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Residues in contact with VAL 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C ALA* 4.5 13.0 - - + -
607C GLY* 3.2 16.9 + - - +
609C ALA* 1.3 79.5 - - + +
611C GLU* 1.3 60.8 + - - +
613C LYS* 3.3 5.9 + - - +
614C GLN* 2.9 56.1 + - + +
781C ASN* 5.4 2.5 - - - +
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Residues in contact with GLU 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C ALA* 5.1 6.5 - - + +
607C GLY 3.1 7.5 + - - +
608C LEU 3.3 2.9 + - - +
610C VAL* 1.3 74.6 - - - +
612C LEU* 1.3 54.1 + - - +
614C GLN* 4.0 7.1 - - + +
615C SER* 2.6 43.5 + - - +
790C ARG* 2.5 51.4 + - - +
794C LEU* 3.2 27.1 - - + +
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Residues in contact with LEU 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C LEU* 2.9 32.7 + - + +
609C ALA 3.6 5.4 - - - +
611C GLU* 1.3 77.1 - - - +
613C LYS* 1.3 55.3 + - - +
615C SER* 3.1 14.1 + - - +
616C THR* 2.6 27.8 + - - +
730C TYR* 3.8 29.6 - - + -
780C LEU* 3.9 29.8 - - + -
793C LEU* 3.8 21.3 - - + -
794C LEU* 3.8 13.5 - - + -
797C ALA* 3.5 32.1 - - + -
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Residues in contact with LYS 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ALA 3.1 14.2 + - - +
610C VAL* 3.3 6.0 + - - +
612C LEU* 1.3 81.7 - - - +
614C GLN* 1.3 59.2 + - + +
616C THR* 3.6 2.2 + - - -
617C ALA* 2.9 36.0 + - + +
730C TYR* 3.6 7.8 + - - -
777C ARG* 5.5 3.6 - - - +
903C HEM 3.5 62.6 + - + +
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Residues in contact with GLN 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C ALA* 5.4 3.8 - - - +
610C VAL* 2.9 46.0 + - + +
611C GLU* 4.0 6.9 - - + +
613C LYS* 1.3 80.1 - - + +
615C SER* 1.3 62.7 + - - +
616C THR 3.3 0.7 + - - -
617C ALA* 3.3 16.3 + - - +
618C GLN 4.8 1.0 + - - -
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Residues in contact with SER 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611C GLU* 2.6 27.4 + - - -
612C LEU* 3.1 13.2 + - - +
614C GLN* 1.3 75.9 - - - +
616C THR* 1.3 65.6 + - - +
617C ALA 3.6 0.2 - - - -
618C GLN* 5.1 3.7 + - - +
619C ALA* 5.5 0.7 + - - +
794C LEU* 4.1 16.6 + - - +
798C THR* 4.1 12.6 + - - -
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Residues in contact with THR 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C LEU 2.6 24.0 + - - +
613C LYS* 3.7 2.8 + - - -
615C SER* 1.3 85.2 - - - +
617C ALA* 1.3 60.1 + - - +
618C GLN 3.2 3.1 - - - -
619C ALA* 3.2 8.3 + - + +
620C HIS* 2.9 30.4 + - - +
730C TYR* 3.9 9.0 + - + -
794C LEU 5.5 0.2 - - - +
797C ALA* 4.2 25.8 - - + -
798C THR* 4.2 8.3 - - - +
801C PHE* 3.5 37.2 - - + -
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Residues in contact with ALA 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C LYS* 2.9 20.9 + - + +
614C GLN* 3.3 13.9 + - - +
616C THR* 1.3 78.0 - - - +
618C GLN* 1.3 61.0 + - - +
620C HIS* 3.5 6.8 + - - +
621C GLU* 3.2 27.9 + - - +
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Residues in contact with GLN 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614C GLN 4.8 1.0 + - - -
615C SER 5.1 3.3 + - - +
616C THR 3.2 0.6 - - - -
617C ALA* 1.3 76.2 - - - +
619C ALA* 1.3 66.0 + - - +
621C GLU* 3.4 8.3 + - - +
622C LYS* 3.3 32.8 + - + +
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Residues in contact with ALA 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C SER 5.5 0.6 + - - +
616C THR* 3.2 13.5 + - + +
618C GLN* 1.3 78.4 - - - +
620C HIS* 1.3 60.5 + - - +
622C LYS* 3.2 12.0 + - - +
623C ALA* 2.9 28.8 + - - +
798C THR* 5.7 3.8 - - + +
801C PHE* 3.7 30.7 - - + -
802C VAL* 6.3 1.6 - - + -
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Residues in contact with HIS 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C THR* 2.9 17.6 + - - +
617C ALA* 3.7 8.3 + - - +
619C ALA* 1.3 78.0 - - - +
621C GLU* 1.3 60.8 + - - +
623C ALA* 3.1 2.5 + - - +
624C GLU* 2.7 57.4 + - + +
801C PHE* 3.7 15.6 - + + -
903C HEM 2.2 91.2 + + + -
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Residues in contact with GLU 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C ALA 3.2 15.4 + - - +
618C GLN* 3.7 10.1 - - - +
619C ALA 3.2 0.4 - - - -
620C HIS* 1.3 85.4 + - - +
622C LYS* 1.3 59.2 + - + +
624C GLU* 3.3 19.0 + - - +
625C HIS* 2.9 57.2 + - + +
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Residues in contact with LYS 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C GLN* 3.3 23.8 + - + +
619C ALA* 3.2 12.7 + - - +
621C GLU* 1.3 76.3 - - + +
623C ALA* 1.3 57.6 + - - +
625C HIS* 3.3 4.2 + - - -
626C SER* 3.0 29.3 + - - -
805C HIS* 4.6 33.9 + - + +
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Residues in contact with ALA 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619C ALA 2.9 13.7 + - - +
620C HIS* 3.4 11.7 - - - +
622C LYS* 1.3 77.9 - - - +
624C GLU* 1.3 62.3 + - - +
625C HIS 3.4 0.2 + - - -
626C SER* 3.5 19.4 + - - -
629C MET* 4.4 9.4 - - - +
801C PHE* 4.4 9.9 - - + +
805C HIS* 5.2 11.2 - - + +
808C PHE* 5.5 2.2 - - - -
903C HEM 3.4 39.7 - - + +
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Residues in contact with GLU 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C HIS* 2.7 35.4 + - + +
621C GLU* 3.3 23.6 - - - +
623C ALA* 1.3 74.1 - - - +
625C HIS* 1.3 82.9 + - + +
626C SER 3.8 0.7 + - - -
629C MET* 4.5 6.2 - - - +
630C SER* 4.7 5.7 + - - -
633C LEU* 5.4 2.4 - - - +
903C HEM 3.4 65.6 - - + +
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Residues in contact with HIS 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621C GLU* 2.9 45.5 + - + +
622C LYS* 3.4 5.8 - - - +
624C GLU* 1.3 108.3 + - + +
626C SER* 1.3 65.0 + - - +
627C THR* 3.6 0.7 + - - -
630C SER* 4.3 10.7 + - - -
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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