Contacts of the helix formed by residues 689 - 708 (chain C) in PDB entry 1S0V
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 VAL 689 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C ILE* 3.6 26.5 - - + -
552C ASP* 4.9 0.4 - - - -
555C GLY* 4.1 11.4 - - - -
558C ALA* 5.1 0.2 - - + -
570C ILE* 3.6 30.3 - - + -
637C LEU* 4.0 27.4 - - + -
685C VAL* 2.9 24.4 + - + +
688C THR* 1.3 90.8 - - + +
690C VAL* 1.3 65.7 + - - +
691C ALA* 2.6 7.1 + - - -
692C ALA* 2.8 15.8 + - + -
693C VAL* 3.3 6.7 + - + +
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Residues in contact with VAL 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C ASP* 3.2 20.4 - - - +
554C VAL* 5.0 6.3 - - + -
685C VAL 4.1 1.6 + - - -
686C SER 4.2 18.2 - - - +
687C VAL* 3.9 20.6 - - - +
688C THR 4.2 2.9 - - - +
689C VAL* 1.3 71.4 - - - +
691C ALA* 1.3 53.7 + - - +
693C VAL* 2.7 35.6 + - + +
694C GLU* 3.0 28.7 + - + +
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Residues in contact with ALA 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C PHE* 4.5 0.2 - - - -
547C SER* 4.0 19.1 - - - +
550C LEU* 4.0 24.8 - - + +
552C ASP* 3.4 31.5 + - + -
689C VAL 2.6 4.6 + - - +
690C VAL* 1.3 72.2 - - - +
692C ALA* 1.3 64.9 + - - +
693C VAL 2.7 5.7 + - - -
694C GLU* 2.9 7.8 + - - +
695C ALA* 2.8 23.2 + - - +
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Residues in contact with ALA 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C ILE* 4.1 26.9 - - + +
546C PHE* 3.4 37.3 - - + +
547C SER 4.8 0.2 - - - +
637C LEU* 4.6 7.9 - - + -
689C VAL* 2.8 16.1 + - + +
691C ALA* 1.3 75.1 - - - +
693C VAL* 1.3 63.1 - - - +
696C MET* 3.1 32.6 + - + +
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Residues in contact with VAL 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637C LEU* 5.7 5.4 - - + -
682C TRP* 4.8 15.5 - - + -
685C VAL* 5.0 0.9 - - + -
686C SER* 3.5 39.5 - - - +
689C VAL* 3.3 10.7 + - + +
690C VAL* 2.7 18.3 + - + +
691C ALA 2.7 3.8 + - - -
692C ALA* 1.3 72.8 - - - +
694C GLU* 1.3 62.4 + - - +
696C MET* 2.9 12.9 + - - +
697C ASN* 2.8 55.8 + - - +
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Residues in contact with GLU 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C LEU* 4.6 1.6 - - + -
690C VAL* 3.1 35.4 - - + +
691C ALA* 2.9 7.9 + - - +
693C VAL* 1.3 83.1 - - - +
695C ALA* 1.3 63.1 + - - +
697C ASN* 3.5 6.1 + - - +
698C TRP* 3.0 24.9 + - - +
865C PRO* 3.9 32.6 - - + +
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Residues in contact with ALA 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C PHE* 3.3 36.8 - - + -
550C LEU* 4.2 15.7 - - + +
691C ALA 2.8 17.4 + - - +
694C GLU* 1.3 75.0 - - - +
696C MET* 1.3 58.4 + - - +
698C TRP* 3.1 5.5 + - - +
699C LEU* 3.0 39.9 + - + +
842C LEU* 4.6 10.1 - - + -
865C PRO* 5.4 0.7 - - - -
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Residues in contact with MET 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C PHE* 3.2 30.7 - - + -
637C LEU* 3.2 47.8 - - + +
638C ALA* 4.2 13.9 - - - +
640C GLY* 4.9 11.4 - - - +
682C TRP* 5.9 2.7 - - + -
692C ALA* 3.1 23.5 + - - +
693C VAL* 2.9 6.1 + - - +
695C ALA* 1.3 76.2 - - - +
697C ASN* 1.3 60.3 + - - +
698C TRP 3.1 0.4 - - - -
700C LYS* 3.1 34.4 + - - +
779C ALA* 3.7 25.4 - - + +
783C VAL* 6.4 0.2 - - - -
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Residues in contact with ASN 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C LYS* 4.4 13.9 + - - -
682C TRP* 5.4 8.0 - - - -
693C VAL* 2.8 42.0 + - - +
694C GLU* 3.7 7.3 - - - +
696C MET* 1.3 77.9 - - - +
698C TRP* 1.3 59.9 + - - +
700C LYS* 3.2 21.6 + - - +
701C SER* 3.1 22.9 + - - -
862C PRO* 5.2 0.7 - - - +
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Residues in contact with TRP 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694C GLU 3.0 17.8 + - - +
695C ALA* 3.1 8.4 + - - +
697C ASN* 1.3 75.3 - - - +
699C LEU* 1.3 87.4 + - + +
700C LYS 2.6 4.5 + - - -
701C SER* 2.5 38.0 + - - -
702C ALA* 3.0 7.3 + - + +
842C LEU* 3.6 33.2 - - + -
845C PHE* 3.5 31.0 - + - -
846C TYR* 4.1 15.3 - + - -
849C PHE* 4.3 8.1 - + - -
861C MET* 4.2 13.2 - - + +
862C PRO* 3.7 13.7 + - + -
863C ALA 3.7 10.8 - - - -
864C LEU* 3.1 60.1 - - + +
865C PRO* 3.7 8.5 - - + -
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Residues in contact with LEU 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C PHE* 4.3 9.0 - - + -
695C ALA 3.0 30.6 + - - +
698C TRP* 1.3 97.6 - - + +
700C LYS* 1.3 56.6 + - - +
702C ALA* 3.9 6.9 - - - +
703C ALA* 3.0 15.9 + - - +
778C ILE* 2.9 36.5 - - + +
779C ALA* 4.5 6.5 - - + -
782C PHE* 3.1 63.9 - - + -
842C LEU* 4.2 7.9 - - + -
845C PHE* 3.8 19.3 - - + -
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Residues in contact with LYS 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640C GLY* 6.1 1.3 - - - -
642C LYS* 4.9 15.2 - - - +
696C MET* 3.1 26.2 + - - +
697C ASN* 3.2 27.6 + - - +
698C TRP 2.6 5.3 + - - -
699C LEU* 1.3 72.6 - - - +
701C SER* 1.3 71.7 + - - +
703C ALA* 3.2 3.6 + - - +
704C LYS* 2.9 22.6 + - - +
775C GLU* 3.0 40.4 - - + +
776C SER 5.6 0.2 - - - +
778C ILE* 3.6 9.3 - - + +
779C ALA* 5.7 1.3 - - + -
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Residues in contact with SER 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697C ASN 3.1 15.4 + - - -
698C TRP 2.5 13.8 + - - -
700C LYS* 1.3 79.6 - - - +
702C ALA* 1.3 56.8 + - - +
704C LYS* 2.5 33.0 + - - +
705C LEU* 3.3 5.0 + - - +
860C LYS* 4.1 18.8 + - - +
861C MET* 3.6 19.5 - - - -
862C PRO* 3.3 21.4 - - - +
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Residues in contact with ALA 702 (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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698C TRP* 3.0 8.6 + - + +
699C LEU* 3.9 13.2 - - - +
701C SER* 1.3 80.2 - - - +
703C ALA* 1.3 67.6 + - - +
705C LEU* 3.0 5.4 + - - +
706C LEU* 3.0 28.9 + - + +
845C PHE* 4.4 7.6 - - + -
849C PHE* 3.9 22.0 - - + -
861C MET* 3.7 26.6 - - + -
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Residues in contact with ALA 703 (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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699C LEU 3.0 18.9 + - - +
700C LYS 3.5 3.6 - - - +
702C ALA* 1.3 78.9 - - - +
704C LYS* 1.3 67.0 + - - +
706C LEU* 3.1 11.7 + - - +
707C ALA* 3.0 20.9 + - - +
725C VAL* 4.4 10.4 - - + +
774C GLN* 3.6 16.4 - - + +
775C GLU* 4.3 3.6 - - - -
778C ILE* 3.4 28.0 - - + +
845C PHE* 5.6 0.6 - - - -
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Residues in contact with LYS 704 (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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700C LYS* 2.9 12.3 + - - +
701C SER* 2.5 23.8 + - - +
703C ALA* 1.3 70.7 - - - +
705C LEU* 1.3 67.0 + - + +
707C ALA* 2.8 16.8 + - - +
708C ALA* 3.0 12.8 + - + +
775C GLU* 2.3 53.6 + - - +
860C LYS* 3.4 31.6 - - - +
5M A 4.5 14.5 + - - -
6M T 3.4 34.8 + - - +
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Residues in contact with LEU 705 (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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701C SER 4.3 8.1 - - - +
702C ALA* 3.0 7.0 + - - +
704C LYS* 1.3 80.6 - - + +
706C LEU* 1.3 55.6 + - - +
707C ALA 2.6 12.5 + - - -
708C ALA* 2.9 18.6 + - + +
720C ARG* 3.1 13.3 + - - -
853C LEU* 4.9 12.1 - - + -
857C GLN* 3.5 53.3 + - + +
860C LYS* 3.6 51.4 - - + +
861C MET* 3.9 16.8 - - + +
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Residues in contact with LEU 706 (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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702C ALA* 3.0 33.4 + - + +
703C ALA* 3.4 10.3 - - - +
705C LEU* 1.3 74.4 - - - +
707C ALA* 1.3 52.9 + - - +
720C ARG* 4.2 8.7 + - - +
723C CYS* 2.2 43.4 + - + +
724C ALA 3.7 7.0 - - - +
725C VAL* 3.1 47.8 - - + -
726C HIS 4.8 0.9 - - - +
849C PHE* 3.4 49.1 - - + -
852C GLN* 4.8 13.2 - - + +
853C LEU* 4.7 8.2 - - + +
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Residues in contact with ALA 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703C ALA 3.0 9.3 + - - +
704C LYS 2.8 10.3 + - - +
705C LEU 2.6 5.7 + - - -
706C LEU* 1.3 75.6 - - - +
708C ALA* 1.3 69.7 + - - +
722C ARG* 2.9 28.3 + - - +
723C CYS 4.0 4.5 - - - +
769C ILE* 4.3 10.1 - - + -
771C ALA* 3.8 33.9 - - + +
774C GLN* 4.6 9.4 - - + -
775C GLU* 5.5 0.2 - - - +
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Residues in contact with ALA 708 (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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704C LYS* 3.0 11.7 + - + +
705C LEU* 2.9 16.8 + - + +
707C ALA* 1.3 86.5 - - - +
709C GLU* 1.3 58.4 + - - +
710C VAL* 3.5 7.9 - - + +
720C ARG* 3.1 19.2 + - - +
722C ARG* 3.6 12.0 - - - +
771C ALA* 5.2 1.3 - - - +
857C GLN* 4.3 12.8 - - - +
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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
------------------------------------------------------------
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