Contacts of the helix formed by residues 694 - 712 (chain C) in PDB entry 3F7F
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 ASN 694 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLU* 4.4 2.9 + - - +
468C ASP* 5.3 4.0 - - + +
469C GLU* 3.0 25.6 - - + +
470C ILE* 3.4 11.5 - - - +
692C PHE* 4.5 0.3 - - - +
693C PHE* 1.3 78.7 + - + +
695C TYR* 1.3 62.9 + - - +
696C GLY* 3.6 4.4 - - - -
697C GLN* 2.6 64.2 + - - +
698C LEU* 3.2 15.6 + - - +
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Residues in contact with TYR 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 4.3 2.1 - - + +
340C LEU* 3.8 28.9 - - + -
341C GLU* 4.1 2.0 - - - +
469C GLU* 2.7 47.1 + - + +
470C ILE* 3.7 18.8 - - + +
471C ILE* 2.8 30.0 + - + +
483C LEU* 5.0 0.4 - - + -
484C TYR 2.7 29.8 + - - -
485C LYS* 3.9 4.7 - - + -
486C LEU* 3.6 49.6 - - + -
694C ASN* 1.3 70.5 - - - +
696C GLY* 1.3 59.4 + - - +
698C LEU* 3.2 14.8 + - + +
699C ILE* 2.8 36.5 + - + +
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Residues in contact with GLY 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLU* 3.8 16.8 + - - -
694C ASN* 3.3 5.3 + - - -
695C TYR* 1.3 79.9 - - - +
697C GLN* 1.3 56.2 + - - +
699C ILE* 3.8 6.6 - - - +
700C ALA* 2.8 32.7 + - - +
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Residues in contact with GLN 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C ASP 4.6 16.6 - - - +
601C PHE* 4.5 5.5 - - - -
602C ILE* 4.3 7.8 + - - +
691C LYS 4.0 2.8 - - - +
692C PHE* 3.6 16.7 - - + +
693C PHE* 2.8 38.7 + - - +
694C ASN* 2.6 53.3 + - - +
696C GLY* 1.3 71.8 - - - -
698C LEU* 1.3 57.7 + - - +
700C ALA* 3.3 6.3 + - - +
701C TYR* 2.9 30.1 + - - +
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Residues in contact with LEU 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C ILE* 5.2 2.0 - - + -
483C LEU* 4.4 13.9 - - + -
485C LYS* 3.6 35.9 - - + -
614C ILE* 4.4 8.5 - - + -
615C SER* 5.0 1.3 - - - +
618C SER* 5.0 2.0 - - - +
692C PHE* 3.5 50.5 - - + +
694C ASN 3.2 11.8 + - - +
695C TYR* 3.2 19.4 + - + +
696C GLY 3.2 0.6 - - - -
697C GLN* 1.3 76.4 - - - +
699C ILE* 1.3 66.5 + - - +
701C TYR* 3.2 5.4 + - + +
702C ILE* 3.0 42.9 + - + +
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Residues in contact with ILE 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLU* 5.7 0.7 - - - +
485C LYS* 4.6 10.3 - - + +
486C LEU* 4.0 38.4 - - + +
487C ASN 4.9 1.3 - - - +
488C THR* 3.9 27.6 - - + +
695C TYR* 2.8 29.0 + - + +
696C GLY* 3.8 6.1 - - - +
698C LEU* 1.3 73.1 - - + +
700C ALA* 1.3 53.8 + - - +
702C ILE* 3.1 8.3 + - + +
703C ASP* 2.8 49.8 + - - +
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Residues in contact with ALA 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C PHE* 4.9 3.2 - - + -
599C LYS* 5.2 8.5 - - + +
600C ASP 6.1 0.2 - - - +
601C PHE* 3.6 17.5 - - + -
696C GLY 2.8 19.1 + - - +
697C GLN* 3.4 7.6 - - - +
698C LEU 3.2 0.2 - - - -
699C ILE* 1.3 78.4 - - - +
701C TYR* 1.3 57.7 + - - +
703C ASP* 3.3 7.6 + - - +
704C SER* 2.8 28.6 + - - -
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Residues in contact with TYR 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C PHE* 3.6 23.1 - + + -
611C THR* 6.1 0.9 - - - -
615C SER* 2.9 36.0 - - - -
680C LEU* 4.0 21.8 - - - +
683C SER* 5.5 4.0 + - - -
686C PHE* 5.4 8.9 + + + +
689C GLY* 4.7 3.8 - - - -
690C VAL* 3.3 47.0 - - + +
692C PHE* 5.0 7.0 - + + -
697C GLN 2.9 17.6 + - - +
698C LEU* 3.7 5.4 - - + +
700C ALA* 1.3 76.7 - - - +
702C ILE* 1.3 61.7 + - + +
704C SER* 3.0 9.9 - - - -
705C LEU* 2.9 55.6 + - + +
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Residues in contact with ILE 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C LYS* 5.4 6.3 - - + +
615C SER* 3.6 42.0 - - - +
618C SER* 3.6 22.2 - - - +
619C LEU* 3.9 26.0 - - + +
622C LEU* 4.3 17.5 - - + -
698C LEU* 3.0 27.5 + - + +
699C ILE* 3.5 8.3 - - - +
701C TYR* 1.3 75.2 - - + +
703C ASP* 1.3 65.4 + - - +
704C SER 2.9 1.1 - - - -
705C LEU* 2.9 11.3 + - + +
706C ASN* 2.9 20.1 + - - +
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Residues in contact with ASP 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C THR* 4.7 6.9 - - - +
590C GLN 5.3 3.8 - - - +
591C MET 5.6 0.7 - - - +
593C PRO* 3.8 21.5 - - + +
596C PHE* 4.1 5.8 - - + -
622C LEU* 4.4 14.3 - - - +
626C HIS* 6.0 0.2 - - - -
699C ILE* 2.8 37.0 + - - +
700C ALA* 3.7 7.2 - - - +
702C ILE* 1.3 73.4 - - - +
704C SER* 1.3 63.0 + - - +
706C ASN* 3.2 11.9 + - - +
707C SER* 3.1 23.9 + - - -
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Residues in contact with SER 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C PHE* 3.2 27.4 - - - -
601C PHE* 4.1 15.0 - - - -
700C ALA 2.8 15.0 + - - -
701C TYR* 3.0 25.2 - - - -
702C ILE 2.9 0.2 - - - -
703C ASP* 1.3 75.1 - - - +
705C LEU* 1.3 62.7 + - - +
707C SER* 3.1 15.4 + - - -
708C ASN* 3.3 18.1 + - - +
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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
----------------------------------------------------------
615C SER* 4.2 19.1 - - - +
616C LEU* 5.4 0.7 - - - +
619C LEU* 4.2 22.7 - - + -
679C LEU* 4.4 25.1 - - + +
680C LEU* 5.1 7.6 - - + -
683C SER* 5.8 3.4 - - - +
701C TYR* 2.9 57.3 + - + +
702C ILE* 2.9 14.3 + - + +
704C SER* 1.3 76.7 - - - +
706C ASN* 1.3 63.5 + - - +
708C ASN* 3.2 21.6 + - - +
709C VAL* 3.1 23.9 + - - +
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Residues in contact with ASN 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C MET 4.0 3.8 - - - +
593C PRO* 4.3 7.3 - - + +
619C LEU* 3.9 10.0 - - + +
622C LEU* 3.6 15.6 - - + +
623C LEU* 3.8 13.0 - - - +
626C HIS* 3.2 26.7 - - - -
702C ILE 2.9 10.8 + - - +
703C ASP* 3.2 18.9 - - - +
704C SER 3.1 0.2 - - - -
705C LEU* 1.3 77.7 - - - +
707C SER* 1.3 57.5 + - - +
709C VAL* 2.8 7.4 + - - +
710C TYR* 2.8 54.5 + - - -
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Residues in contact with SER 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C PRO* 2.9 30.1 - - - +
594C GLY 4.0 4.0 + - - -
596C PHE* 3.3 20.9 - - - -
703C ASP 3.1 8.5 + - - -
704C SER 3.1 7.7 + - - -
706C ASN* 1.3 75.4 - - - +
708C ASN* 1.3 60.9 + - - +
710C TYR* 3.0 3.0 + - - +
711C ASN* 2.7 52.5 + - - +
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Residues in contact with ASN 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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596C PHE* 5.3 2.4 - - - -
679C LEU* 4.8 11.9 + - + +
682C ASP* 4.0 25.2 + - - +
683C SER* 4.7 17.8 - - - +
704C SER* 3.3 16.7 + - - +
705C LEU* 3.2 25.8 + - - +
707C SER* 1.3 77.7 - - - +
709C VAL* 1.3 62.3 + - + +
711C ASN* 4.6 3.5 + - - +
712C ALA* 3.2 24.3 + - - +
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Residues in contact with VAL 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619C LEU* 4.3 10.1 - - + -
623C LEU* 3.9 22.4 - - + -
660C LYS* 3.6 24.1 - - + +
664C LEU* 4.1 37.9 - - + -
679C LEU* 4.5 12.1 - - + -
705C LEU 3.1 14.5 + - - +
706C ASN* 2.8 9.4 + - - +
708C ASN* 1.3 78.8 - - - +
710C TYR* 1.3 71.3 + - + +
711C ASN 3.5 0.3 + - - -
712C ALA* 3.6 13.1 + - - +
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Residues in contact with TYR 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C MET* 3.7 11.8 - - - +
592C LYS* 4.4 13.1 - - + -
593C PRO* 3.9 16.6 - - + -
623C LEU* 3.3 15.0 - - + +
626C HIS* 2.6 31.8 + - - -
656C ASP* 4.7 0.2 - - - +
657C LEU* 3.4 40.7 - - + +
660C LYS* 2.9 32.9 + - + +
661C GLN* 3.0 30.5 + - + -
706C ASN* 2.8 37.8 + - - +
707C SER* 3.0 5.1 + - - +
709C VAL* 1.3 84.0 - - + +
711C ASN* 1.3 61.8 + - - +
712C ALA 3.4 0.2 - - - -
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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
----------------------------------------------------------
660C LYS* 4.8 0.7 - - - +
707C SER* 2.7 37.9 + - - +
708C ASN* 4.1 3.1 - - - +
710C TYR* 1.3 75.2 - - - +
712C ALA* 1.3 68.3 + - - +
713C SER* 3.5 1.7 + - - -
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Residues in contact with ALA 712 (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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660C LYS* 3.5 22.2 + - + -
682C ASP* 6.0 1.1 - - - +
708C ASN 3.2 19.1 + - - +
709C VAL* 3.8 11.4 - - - +
710C TYR 3.4 1.4 - - - -
711C ASN* 1.3 81.9 - - - +
713C SER* 1.3 67.5 + - - +
714C ILE* 5.4 3.1 - - + -
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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