Contacts of the helix formed by residues 596 - 604 (chain C) in PDB entry 6T8G
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 GLU 596 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C LYS* 3.4 7.1 + - - -
499C PRO* 3.2 32.6 - - + +
500C LYS* 3.5 22.7 + - + +
594C VAL* 4.0 1.6 - - - -
595C ASP* 1.3 80.9 - - + +
597C PHE* 1.3 61.4 + - - +
598C ALA* 3.3 19.8 + - - +
599C ASP* 3.5 26.2 + - - +
600C MET* 3.6 5.5 + - - +
629C ALA 3.6 0.4 - - - -
631C GLN* 2.9 48.9 + - - +
632C ARG* 5.3 2.3 + - - +
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Residues in contact with PHE 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C LEU* 5.8 4.0 - - + -
594C VAL* 3.7 11.1 - - + +
596C GLU* 1.3 71.3 - - - +
598C ALA* 1.3 58.4 + - - +
600C MET* 3.2 16.4 + - - +
601C MET* 3.0 58.5 + - + +
608C VAL* 4.2 18.8 - - + -
609C GLU* 5.3 1.6 - - - -
612C ILE* 4.2 12.6 - - + -
628C LEU* 4.2 21.1 - - + -
629C ALA 3.0 26.4 + - - +
630C THR* 4.6 3.6 - - - +
637C VAL* 3.7 19.5 - - + -
638C ILE* 5.8 1.1 - - + -
642C ILE* 3.6 40.4 - - + -
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Residues in contact with ALA 598 (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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644B ALA* 6.3 0.2 - - + -
596C GLU* 3.2 21.0 + - + +
597C PHE* 1.3 78.7 - - - +
599C ASP* 1.3 61.2 + - - +
601C MET* 3.4 5.0 + - - +
602C MET* 2.9 28.9 + - - +
630C THR* 4.3 10.6 + - - +
632C ARG* 3.5 32.1 + - + +
637C VAL* 4.1 19.6 - - + +
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Residues in contact with ASP 599 (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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617B GLN* 3.0 28.6 + - - +
641B LEU* 5.9 1.2 - - - -
644B ALA* 3.2 31.6 - - - +
645B ASN* 3.9 8.4 + - - -
499C PRO* 4.3 3.1 - - + -
500C LYS* 3.8 5.2 + - - -
521C MET* 4.0 11.7 - - + -
596C GLU* 3.5 24.4 + - + +
597C PHE 3.4 0.4 - - - -
598C ALA* 1.3 77.8 - - - +
600C MET* 1.3 60.1 + - - +
602C MET* 4.1 7.1 - - - +
603C ILE* 2.9 39.9 + - + +
632C ARG* 5.5 0.2 + - - -
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Residues in contact with MET 600 (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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497C ILE* 3.7 32.5 - - + -
499C PRO* 5.0 1.6 - - + -
521C MET* 3.6 27.1 - - + +
524C ALA* 5.0 4.0 - - + -
528C LEU* 4.7 12.1 - - + -
594C VAL* 3.7 32.1 - - + -
596C GLU 3.6 4.4 + - - +
597C PHE* 3.2 23.1 + - + +
598C ALA 3.2 0.6 - - - -
599C ASP* 1.3 79.9 - - - +
601C MET* 1.3 59.6 + - - +
604C VAL* 2.8 27.9 + - - +
608C VAL* 3.7 33.8 - - + +
612C ILE* 5.5 3.4 - - - -
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Residues in contact with MET 601 (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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597C PHE* 3.0 45.1 + - + +
598C ALA* 3.9 4.0 - - - +
600C MET* 1.3 76.3 - - - +
602C MET* 1.3 64.0 + - - +
604C VAL 3.0 22.0 - - - +
605C GLY* 3.3 15.2 - - - +
606C LYS* 6.0 1.1 - - - +
608C VAL* 5.1 3.6 - - + -
609C GLU* 3.3 38.1 - - + +
636C ASP 3.4 20.2 - - - +
637C VAL* 3.2 32.8 - - + +
639C THR* 4.7 1.6 - - + -
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Residues in contact with MET 602 (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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640B GLY* 3.7 46.0 - - - +
641B LEU* 4.2 10.2 - - + +
644B ALA* 5.7 1.8 - - + -
598C ALA 2.9 19.3 + - - +
599C ASP* 3.2 11.4 + - - +
601C MET* 1.3 79.2 - - - +
603C ILE* 1.3 64.5 + - + +
605C GLY 5.3 0.2 + - - -
632C ARG* 5.1 12.6 - - - +
14G T 6.0 1.8 - - - +
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Residues in contact with ILE 603 (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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613B ALA* 5.9 3.8 - - + -
614B ARG* 6.3 2.9 - - - -
617B GLN* 5.0 11.0 - - - +
641B LEU* 4.2 32.3 - - + -
645B ASN* 6.3 0.7 - - - +
520C ASP* 4.9 4.9 - - - +
521C MET* 3.7 35.7 - - + +
522C LYS* 3.9 32.2 + - + +
599C ASP* 2.9 20.4 + - + +
602C MET* 1.3 80.5 - - + +
604C VAL* 1.3 59.9 + - - +
605C GLY 3.8 1.9 + - - -
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Residues in contact with VAL 604 (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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521C MET* 3.8 31.0 - - + +
522C LYS* 3.4 28.9 - - + +
525C ALA* 5.9 3.6 - - + -
600C MET 2.8 20.8 + - - +
601C MET* 3.0 9.0 - - - +
603C ILE* 1.3 74.2 - - - +
605C GLY* 1.3 64.4 + - - +
606C LYS 4.5 0.2 - - - +
607C LYS* 3.9 32.1 - - + +
608C VAL* 3.8 29.3 - - + +
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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