Contacts of the helix formed by residues 668 - 672 (chain D) 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 GLY 668 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398D ARG* 4.4 16.7 + - - -
657D LYS* 4.4 11.6 - - - +
660D SER* 3.1 3.0 + - - -
667D GLY* 1.3 74.8 - - - -
669D ALA* 1.3 58.8 + - - +
670D GLU* 3.0 12.4 + - - +
671D GLN* 3.1 26.0 + - - +
672D LEU* 4.8 0.3 + - - +
679D LEU* 4.5 6.9 - - - +
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Residues in contact with ALA 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651D ALA* 4.4 8.5 - - + -
652D PHE 4.0 4.8 - - - +
653D GLN* 4.2 1.4 - - - -
654D VAL* 3.4 32.6 + - + +
660D SER* 2.9 22.6 + - - +
663D ILE* 5.9 0.2 - - + -
664D LEU* 3.8 22.8 - - + +
667D GLY 3.8 0.4 - - - -
668D GLY* 1.3 73.3 - - - +
670D GLU* 1.3 63.9 + - - +
671D GLN 3.2 0.6 + - - -
672D LEU* 4.2 6.4 + - - +
679D LEU* 3.7 16.2 - - + +
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Residues in contact with GLU 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653D GLN* 4.2 8.5 + - - +
654D VAL* 3.8 15.8 - - - +
655D SER 4.1 15.3 - - - +
656D SER* 4.3 13.5 - - - -
657D LYS* 3.3 35.6 + - + +
660D SER* 4.3 5.5 - - - -
668D GLY 3.0 0.6 + - - +
669D ALA* 1.3 79.3 - - - +
671D GLN* 1.3 72.8 + - + +
672D LEU 3.2 11.9 + - - +
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Residues in contact with GLN 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D SER 5.4 2.0 + - - -
385D ALA* 3.7 22.9 - - - +
396D SER* 3.0 27.5 + - - -
397D VAL 3.4 8.6 - - - +
398D ARG* 3.4 44.9 + - + +
399D VAL* 3.9 5.4 + - - +
657D LYS* 5.4 7.2 - - + +
668D GLY* 3.1 17.2 + - - +
670D GLU* 1.3 97.4 + - + +
672D LEU* 1.3 64.1 + - - +
673D LEU* 4.8 1.4 - - - +
690D ARG* 5.2 1.7 + - - -
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Residues in contact with LEU 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D ILE* 5.4 2.1 - - - +
396D SER* 3.6 8.1 + - - -
398D ARG* 4.4 6.1 - - - -
651D ALA 3.9 7.0 - - - +
652D PHE 3.9 13.0 - - - +
653D GLN* 3.7 28.1 + - + -
669D ALA* 4.4 6.1 - - - +
670D GLU 3.2 4.8 + - - +
671D GLN* 1.3 85.2 - - - +
673D LEU* 1.3 66.8 + - - +
677D ASP* 3.3 37.0 - - + +
679D LEU* 3.7 39.9 - - + -
690D ARG* 3.6 32.8 - - + +
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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
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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