Contacts of the helix formed by residues 697 - 712 (chain B) in PDB entry 6T8B
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B ASP* 3.3 22.6 + - - -
422B ARG* 4.5 1.9 + - - +
695B PHE* 3.6 32.6 + - - -
696B VAL* 1.3 77.0 - - - +
698B ASP* 1.3 61.0 + - - +
699B ASP* 3.9 12.2 + - - +
700B GLU* 2.9 33.8 + - - +
701B VAL* 3.5 3.3 + - - +
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Residues in contact with ASP 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A ARG* 2.9 58.8 + - - +
477B ASN* 4.9 0.9 + - - -
506B ILE* 4.7 2.7 - - + +
696B VAL 4.5 2.8 - - - +
697B SER* 1.3 71.0 - - - +
699B ASP* 1.3 65.4 + - - +
700B GLU 3.2 0.2 - - - -
701B VAL* 3.8 7.4 - - + +
702B HIS* 2.9 47.8 + - + +
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Residues in contact with ASP 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 4.9 4.5 - - - +
697B SER* 3.1 12.1 + - - +
698B ASP* 1.3 78.9 - - - +
700B GLU* 1.3 61.3 + - - +
702B HIS* 3.8 6.0 - - - +
703B ARG* 2.9 45.7 + - - +
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Residues in contact with GLU 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU 5.4 0.2 - - - +
321B LEU* 3.6 26.4 - - + +
322B ASP* 3.1 22.9 + - - +
422B ARG* 2.3 33.6 + - - -
423B PHE* 4.3 5.3 + - - +
424B SER 5.5 0.7 + - - -
481B LEU* 4.6 0.4 - - - -
695B PHE 4.2 1.0 - - - +
696B VAL* 3.3 31.5 - - + +
697B SER* 2.9 14.2 + - - +
699B ASP* 1.3 75.5 - - - +
701B VAL* 1.3 58.2 + - - +
703B ARG* 3.3 26.6 + - - +
704B VAL* 2.9 35.9 + - - +
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Residues in contact with VAL 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ASN* 4.4 10.5 - - + +
481B LEU* 3.8 13.9 - - + -
506B ILE* 3.5 29.2 - - + -
507B TYR* 3.7 32.8 - - + +
696B VAL* 3.6 28.5 - - + +
697B SER 3.5 4.9 + - - +
698B ASP* 3.3 12.2 + - - +
700B GLU* 1.3 72.8 - - - +
702B HIS* 1.3 62.4 + - - +
704B VAL* 3.3 5.8 + - - +
705B VAL* 2.9 31.1 + - + +
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Residues in contact with HIS 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLY* 4.2 18.4 + - - -
506B ILE* 3.8 39.8 + - + +
698B ASP* 2.9 44.8 + - + +
699B ASP* 3.8 6.7 - - - +
701B VAL* 1.3 76.6 - - - +
703B ARG* 1.3 57.7 + - + +
705B VAL* 3.3 5.2 + - - +
706B GLU* 2.9 39.3 + - + +
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Residues in contact with ARG 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LEU* 3.1 47.3 + - + +
321B LEU 3.4 12.5 + - - -
322B ASP* 2.5 37.6 + - - -
699B ASP* 2.9 29.5 + - - +
700B GLU* 3.4 23.5 - - - +
701B VAL 3.3 0.2 - - - -
702B HIS* 1.3 77.0 - - + +
704B VAL* 1.3 57.7 + - - +
706B GLU* 3.3 7.7 + - - +
707B ALA* 2.9 23.6 + - - +
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Residues in contact with VAL 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PRO* 5.5 0.4 - - + -
320B LEU* 3.8 12.1 - - + -
321B LEU* 4.2 4.7 - - + -
481B LEU* 3.9 18.4 - - + -
484B LEU* 3.9 16.6 - - + -
485B PHE* 3.4 36.8 - - + -
700B GLU 2.9 22.3 + - - +
701B VAL* 3.7 6.1 - - + +
703B ARG* 1.3 76.7 - - - +
705B VAL* 1.3 57.6 + - + +
707B ALA* 3.1 3.0 + - - +
708B TRP* 2.9 56.1 + - + +
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Residues in contact with VAL 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 5.6 0.4 - - + -
506B ILE 3.4 28.5 - - - +
507B TYR* 3.8 28.5 - - + -
508B GLU 4.4 6.5 - - - +
510B ILE* 3.8 22.0 - - + -
701B VAL* 2.9 23.2 + - + +
702B HIS* 3.9 5.6 - - - +
704B VAL* 1.3 78.3 - - + +
706B GLU* 1.3 60.9 + - - +
708B TRP* 3.2 1.7 + - - +
709B LYS* 2.9 45.0 + - + +
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Residues in contact with GLU 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B HIS* 2.9 27.3 + - + +
703B ARG* 3.7 7.2 - - - +
705B VAL* 1.3 79.2 - - + +
707B ALA* 1.3 61.2 + - - +
708B TRP 3.5 0.2 + - - -
709B LYS* 3.7 27.0 + - - +
710B LEU* 3.6 28.4 + - + +
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Residues in contact with ALA 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B PRO* 4.6 9.2 - - + -
317B PRO* 6.1 0.4 - - + -
320B LEU* 3.7 19.5 - - + -
703B ARG 2.9 14.3 + - - +
704B VAL* 3.1 8.0 + - - +
706B GLU* 1.3 78.3 - - - +
708B TRP* 1.3 61.9 + - - +
710B LEU* 3.6 5.1 + - - +
711B ARG* 3.2 43.7 + - - +
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Residues in contact with TRP 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B THR 4.7 8.1 - - - -
315B LEU* 4.0 8.5 - - + -
316B PRO* 3.3 33.5 - - + +
484B LEU* 3.0 47.9 - - + +
487B SER 3.8 9.6 - - - -
488B THR* 4.7 1.6 - - + -
489B PRO* 4.2 15.0 - - + -
510B ILE* 3.8 22.2 - - + -
511B PRO* 3.6 23.2 - - + +
512B HIS* 3.3 30.5 - + - -
704B VAL* 2.9 42.5 + - + +
705B VAL* 3.2 1.5 + - - +
707B ALA* 1.3 74.6 - - - +
709B LYS* 1.3 58.2 + - - +
710B LEU 2.9 11.4 + - - -
711B ARG* 3.2 20.8 + - + -
712B GLY 3.3 13.5 + - - +
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Residues in contact with LYS 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B GLU 4.2 13.5 + - - +
509B GLY* 3.8 31.2 - - - +
510B ILE 4.2 0.2 - - - +
705B VAL* 2.9 37.1 + - + +
706B GLU* 3.7 25.1 + - - +
707B ALA 3.5 0.4 - - - -
708B TRP* 1.3 75.1 - - - +
710B LEU* 1.3 65.3 + - + +
712B GLY 3.6 11.6 - - - +
714B PRO* 5.2 9.3 - - + +
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Residues in contact with LEU 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B GLU* 3.6 18.4 + - + +
707B ALA* 3.6 7.6 + - - +
708B TRP 2.9 0.6 - - - -
709B LYS* 1.3 87.2 - - + +
711B ARG* 1.3 62.6 + - + +
712B GLY 3.1 7.9 + - - +
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Residues in contact with ARG 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B THR* 3.0 49.1 + - - +
315B LEU 3.8 3.8 + - - -
316B PRO* 3.8 26.2 - - - +
317B PRO* 3.4 26.1 - - - +
489B PRO* 6.0 1.0 - - - +
511B PRO* 5.3 1.3 - - - -
707B ALA* 3.2 24.5 + - - +
708B TRP* 3.2 16.5 + - + +
710B LEU* 1.3 75.9 - - + +
712B GLY* 1.3 54.9 + - - +
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Residues in contact with GLY 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B PRO* 5.7 2.0 - - - -
511B PRO* 4.1 15.5 - - - +
708B TRP 3.3 13.9 + - - +
709B LYS* 3.6 14.2 - - - +
710B LEU 3.1 4.3 + - - -
711B ARG* 1.3 79.3 - - - +
713B ALA* 1.3 66.7 + - - -
714B PRO* 3.8 1.6 - - - +
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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