Contacts of the helix formed by residues 703 - 720 (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 SER 703 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C GLN* 2.9 18.8 + - - +
701C THR 3.6 1.2 + - - -
702C ALA* 1.3 76.2 - - - +
704C PRO* 1.3 76.6 - - - +
705C ALA* 3.6 5.4 + - - +
706C VAL* 3.0 26.0 + - - +
707C ILE* 2.9 20.8 + - - +
807C VAL* 5.2 1.4 + - - +
810C ASP* 3.7 17.6 + - - +
811C LEU* 6.4 1.3 - - - -
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Residues in contact with PRO 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C ALA 4.6 0.9 - - - +
703C SER* 1.3 83.5 - - - +
705C ALA* 1.3 60.8 + - - +
707C ILE* 3.3 16.5 + - + +
708C ASP* 3.1 28.7 + - - +
810C ASP* 3.1 16.6 - - - +
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Residues in contact with ALA 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703C SER* 4.0 1.3 - - - +
704C PRO* 1.3 76.7 - - - +
706C VAL* 1.3 59.7 + - - +
708C ASP* 3.4 9.6 + - - +
709C TYR* 3.0 27.9 + - - +
803C PHE* 4.8 3.5 - - - +
806C GLN* 3.4 47.2 - - + +
807C VAL* 3.7 9.6 - - + +
810C ASP* 3.1 18.2 + - - +
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Residues in contact with VAL 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C GLN* 3.1 44.6 - - + +
651C LEU* 4.0 15.0 - - + -
652C PHE* 4.2 9.0 - - + -
702C ALA* 3.9 13.9 - - + -
703C SER* 3.0 13.7 + - - +
705C ALA* 1.3 75.6 - - - +
707C ILE* 1.3 60.0 + - - +
709C TYR* 3.7 5.6 - - - +
710C VAL* 2.8 44.7 + - + +
807C VAL* 3.9 21.3 - - + -
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Residues in contact with ILE 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLU* 5.6 5.6 - - - +
702C ALA* 3.7 25.6 - - + +
703C SER 2.9 19.1 + - - +
704C PRO* 3.3 15.5 + - + +
706C VAL* 1.3 76.7 - - - +
708C ASP* 1.3 61.9 + - - +
710C VAL* 3.8 4.1 - - - +
711C ASN* 2.9 50.8 + - - +
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Residues in contact with ASP 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C PRO* 3.1 19.5 + - - +
705C ALA* 3.8 9.0 - - - +
707C ILE* 1.3 78.5 - - - +
709C TYR* 1.3 66.9 + - - +
711C ASN* 3.3 10.1 + - - +
712C ARG* 3.0 23.0 + - - +
803C PHE* 3.8 16.4 - - + -
806C GLN* 5.3 6.2 + - - +
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Residues in contact with TYR 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C PHE* 3.5 46.2 - + + -
656C LEU* 5.5 1.6 - - - +
705C ALA 3.0 18.0 + - - +
706C VAL* 3.7 4.9 - - - +
708C ASP* 1.3 74.7 - - - +
710C VAL* 1.3 65.3 + - - +
712C ARG* 3.2 3.8 + - - +
713C LEU* 3.0 40.7 + - + +
728C HIS* 3.8 28.4 + + - -
732C ARG* 3.4 22.2 - - - +
800C ALA* 5.5 0.2 - - - +
803C PHE* 3.7 33.6 - + + -
804C ASN* 3.0 34.2 + - - -
807C VAL* 4.0 11.7 - - + -
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Residues in contact with VAL 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B SER* 5.3 0.9 - - - +
394B SER* 4.1 5.8 - - - +
395B GLU* 5.9 2.5 - - + +
651C LEU* 3.9 23.8 - - + +
652C PHE* 4.0 10.3 - - + -
655C ALA* 3.9 13.5 - - + -
706C VAL* 2.8 37.0 + - + +
707C ILE* 3.8 4.7 - - - +
709C TYR* 1.3 73.6 - - - +
711C ASN* 1.3 64.9 + - - +
713C LEU* 3.1 3.9 + - - +
714C GLU* 2.9 47.5 + - - +
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Residues in contact with ASN 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B SER* 5.5 0.3 + - - -
395B GLU* 5.2 5.4 - - - +
707C ILE* 2.9 40.6 + - - +
708C ASP* 3.7 10.6 + - - +
710C VAL* 1.3 77.2 - - - +
712C ARG* 1.3 64.1 + - - +
714C GLU* 3.3 16.6 + - - +
715C GLU* 3.0 33.6 + - - +
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Residues in contact with ARG 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C ASP 3.0 13.1 + - - +
709C TYR 3.2 7.8 + - - +
711C ASN* 1.3 77.7 - - - +
713C LEU* 1.3 58.1 + - - +
715C GLU* 3.0 40.3 + - - +
716C ILE* 2.9 39.7 + - + +
719C ASN* 5.1 6.3 - - - +
721C ASP* 4.1 17.8 + - - -
724C ALA* 4.1 3.6 - - - +
728C HIS* 4.3 3.8 - - + +
792C HIS* 4.2 7.5 - - - -
796C GLU* 2.9 43.3 + - - +
803C PHE* 3.7 26.7 - - + -
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Residues in contact with LEU 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C PHE* 3.5 30.1 - - + +
655C ALA* 4.0 20.1 - - + +
656C LEU* 3.7 26.9 - - + +
659C ALA* 3.6 9.6 - - + +
709C TYR* 3.0 40.3 + - + +
710C VAL 3.6 5.2 - - - +
712C ARG* 1.3 76.2 - - - +
714C GLU* 1.3 58.1 + - - +
716C ILE* 3.4 8.2 + - + +
717C ARG* 3.0 26.7 + - - +
725C LEU* 5.4 0.7 - - + -
728C HIS* 3.8 36.3 - - + +
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Residues in contact with GLU 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B SER* 2.9 23.9 + - - -
394B SER* 2.8 40.2 + - - -
655C ALA* 4.6 8.9 - - + +
658C GLN* 5.0 0.2 - - - +
710C VAL* 2.9 30.5 + - + +
711C ASN* 3.8 14.8 - - - +
713C LEU* 1.3 74.3 - - - +
715C GLU* 1.3 60.7 + - - +
717C ARG* 3.3 32.2 + - - +
718C ASP* 2.9 38.0 + - - +
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Residues in contact with GLU 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711C ASN* 3.0 24.4 + - - +
712C ARG* 3.0 41.3 + - - +
714C GLU* 1.3 75.6 - - - +
716C ILE* 1.4 60.4 + - - +
718C ASP* 3.2 5.4 + - - -
719C ASN* 2.8 46.6 + - - +
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Residues in contact with ILE 716 (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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659C ALA* 4.3 8.5 - - + -
663C VAL* 4.9 2.2 - - + +
712C ARG* 2.9 34.7 + - + +
713C LEU* 3.6 12.3 - - + +
714C GLU 3.3 0.2 - - - -
715C GLU* 1.4 74.1 - - - +
717C ARG* 1.3 58.9 + - - +
719C ASN* 4.8 0.4 - - - +
720C VAL* 2.9 24.6 + - - -
721C ASP* 3.1 38.1 + - + +
724C ALA* 3.8 13.5 - - + +
725C LEU* 3.7 19.5 - - + -
728C HIS* 3.3 38.1 - - + +
796C GLU* 3.7 10.1 - - - +
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Residues in contact with ARG 717 (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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388B ASP* 5.9 2.4 - - - +
392B GLY 4.5 13.7 + - - -
393B SER* 5.1 2.2 - - - +
394B SER 5.1 3.2 - - - +
655C ALA 5.5 0.2 - - - +
658C GLN* 2.8 60.7 + - - +
659C ALA* 3.8 14.8 - - - +
662C ALA* 3.9 16.9 - - + +
663C VAL* 5.9 0.2 - - - -
713C LEU 3.0 14.5 + - - +
714C GLU* 3.4 37.3 + - - +
716C ILE* 1.3 77.6 - - - +
718C ASP* 1.3 93.4 + - - +
720C VAL* 3.2 20.5 + - - +
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Residues in contact with ASP 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714C GLU* 2.9 24.9 + - - +
715C GLU* 3.9 4.8 - - - +
717C ARG* 1.3 106.5 + - - +
719C ASN* 1.3 64.6 + - - +
720C VAL* 3.6 6.8 + - - +
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Residues in contact with ASN 719 (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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712C ARG* 5.1 5.5 - - - +
715C GLU* 2.8 33.8 + - - +
716C ILE* 4.3 2.2 - - - +
718C ASP* 1.3 81.5 - - - +
720C VAL* 1.3 71.4 + - - +
721C ASP* 4.1 13.6 + - + +
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Residues in contact with VAL 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662C ALA* 3.9 17.5 - - + +
663C VAL* 4.3 11.0 - - + -
666C SER* 3.7 32.8 - - - +
716C ILE 2.9 9.1 + - - -
717C ARG 3.2 13.9 + - - +
718C ASP 4.0 6.7 - - - +
719C ASN* 1.3 81.9 - - - +
721C ASP* 1.3 58.7 + - - +
722C GLY 3.2 7.0 + - - -
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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
------------------------------------------------------------
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