Contacts of the helix formed by residues 697 - 710 (chain C) in PDB entry 6T8O
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 697 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C ASP* 4.2 7.6 + - - -
695C PHE* 4.2 17.9 - - - -
696C VAL* 1.3 77.5 - - - +
698C ASP* 1.3 66.4 + - - +
699C ASP* 3.7 10.6 + - - +
700C GLU* 3.3 33.1 + - - +
701C VAL* 3.1 27.8 + - - +
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Residues in contact with ASP 698 (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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548B ARG* 5.9 4.4 + - - +
477C ASN* 5.8 1.7 + - - -
506C ILE* 4.4 13.1 - - + +
696C VAL 5.5 0.2 - - - +
697C SER* 1.3 73.9 - - - +
699C ASP* 1.3 61.5 + - - +
701C VAL* 3.9 8.0 - - - +
702C HIS* 2.9 32.1 + - - +
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Residues in contact with ASP 699 (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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322C ASP* 5.2 7.2 - - - +
697C SER* 3.2 10.3 + - - +
698C ASP* 1.3 80.5 - - - +
700C GLU* 1.3 59.4 + - + +
702C HIS* 3.5 5.0 + - - +
703C ARG* 2.9 46.1 + - - +
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Residues in contact with GLU 700 (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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320C LEU* 5.2 0.6 - - - +
321C LEU* 3.7 29.8 - - + +
322C ASP* 2.8 51.3 + - - +
422C ARG* 4.6 3.8 + - - -
423C PHE* 4.7 6.3 - - - +
481C LEU* 4.6 1.3 - - + -
695C PHE 4.6 2.8 - - - +
696C VAL* 3.6 23.5 - - + +
697C SER* 3.3 23.9 + - - +
699C ASP* 1.3 73.9 - - + +
701C VAL* 1.3 60.2 + - - +
703C ARG* 3.3 12.6 + - - +
704C VAL* 2.9 35.5 + - - +
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Residues in contact with VAL 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C ASN* 4.6 7.9 - - + +
481C LEU* 3.8 18.2 - - + -
506C ILE* 3.8 23.8 - - + -
507C TYR* 3.6 32.3 - - + +
696C VAL* 3.7 27.1 - - + -
697C SER 3.1 18.1 + - - +
698C ASP* 4.0 7.2 - - - +
700C GLU* 1.3 74.3 - - - +
702C HIS* 1.3 58.4 + - - +
704C VAL* 3.2 3.1 + - - +
705C VAL* 2.9 33.1 + - - +
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Residues in contact with HIS 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ARG* 5.0 7.9 + - - -
506C ILE* 4.3 21.8 - - + +
698C ASP 2.9 20.5 + - - +
699C ASP* 3.9 5.6 - - - +
701C VAL* 1.3 76.4 - - - +
703C ARG* 1.3 58.2 + - - +
705C VAL* 3.4 8.6 + - + +
706C GLU* 2.9 64.8 + - + +
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Residues in contact with ARG 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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320C LEU* 2.5 66.1 + - + +
321C LEU 4.5 0.2 - - - -
322C ASP* 4.4 11.7 + - - -
699C ASP* 2.9 36.9 + - - +
700C GLU* 3.6 18.3 - - - +
701C VAL 3.2 0.4 - - - -
702C HIS* 1.3 75.6 - - - +
704C VAL* 1.3 60.3 + - - +
706C GLU* 3.4 5.0 + - + +
707C ALA* 2.9 29.2 + - + +
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Residues in contact with VAL 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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316C PRO* 5.7 1.6 - - + -
320C LEU* 4.8 9.2 - - + -
321C LEU* 5.0 2.9 - - + -
481C LEU* 3.9 16.6 - - + -
484C LEU* 3.8 26.5 - - + -
485C PHE* 3.7 35.7 - - + -
507C TYR* 6.4 0.2 - - + -
700C GLU 2.9 21.6 + - - +
701C VAL 3.2 5.1 + - - +
703C ARG* 1.3 75.1 - - - +
705C VAL* 1.3 57.9 + - + +
707C ALA* 3.3 5.5 + - - +
708C TRP* 3.0 55.3 + - + +
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Residues in contact with VAL 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C LEU* 5.8 1.1 - - + -
506C ILE* 3.3 29.2 - - + +
507C TYR* 3.6 29.4 - - + -
508C GLU 5.3 0.9 - - - +
510C ILE* 4.2 19.2 - - + +
701C VAL* 2.9 22.8 + - + +
702C HIS* 3.7 10.1 - - + +
703C ARG 3.3 0.2 - - - -
704C VAL* 1.3 78.8 - - + +
706C GLU* 1.3 62.9 + - - +
708C TRP* 3.3 2.8 + - - +
709C LYS* 2.9 47.1 + - + +
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Residues in contact with GLU 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 HIS* 2.9 54.0 + - + +
703C ARG* 4.0 5.2 - - + +
705C VAL* 1.3 77.8 - - - +
707C ALA* 1.3 57.9 + - - +
709C LYS* 3.8 30.6 + - - +
710C LEU* 2.9 43.5 + - + +
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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
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316C PRO* 4.7 4.0 - - + -
320C LEU* 4.0 22.4 - - + -
703C ARG* 2.9 18.5 + - + +
704C VAL* 3.7 4.7 - - - +
705C VAL 3.3 0.2 - - - -
706C GLU* 1.3 77.1 - - - +
708C TRP* 1.3 56.9 + - - +
710C LEU* 3.4 8.7 + - - +
711C ARG* 2.9 48.4 + - - +
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Residues in contact with TRP 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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315C LEU* 4.0 21.3 - - + -
316C PRO* 3.6 33.5 - - + +
484C LEU* 3.3 43.5 + - + +
487C SER 4.1 5.6 - - - -
488C THR* 4.6 2.5 - - + -
489C PRO* 4.0 13.7 - - + -
510C ILE* 4.4 8.5 - - + -
511C PRO* 3.4 32.9 - - + +
512C HIS* 3.6 27.4 - + - -
704C VAL* 3.0 40.1 + - + +
705C VAL* 3.9 3.8 - - - +
707C ALA* 1.3 75.6 - - - +
709C LYS* 1.3 59.9 + - - +
711C ARG* 3.1 33.7 - - + +
712C GLY* 3.0 23.7 + - - -
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Residues in contact with LYS 709 (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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508C GLU 4.3 8.9 + - - +
509C GLY* 3.3 36.6 - - - +
510C ILE 4.3 0.4 - - - +
705C VAL* 2.9 38.6 + - + +
706C GLU* 3.3 28.7 + - - +
708C TRP* 1.3 76.6 - - - +
710C LEU* 1.3 63.9 + - + +
712C GLY 3.5 16.6 + - - +
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Residues in contact with LEU 710 (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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706C GLU* 2.9 30.4 + - + +
707C ALA* 3.9 7.2 - - - +
709C LYS* 1.3 78.6 - - + +
711C ARG* 1.3 59.2 + - - +
712C GLY 3.7 1.3 - - - -
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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
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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