Contacts of the helix formed by residues 657 - 664 (chain D) 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 LYS 657 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656D SER* 1.3 73.7 - - - +
658D ILE* 1.3 72.4 + - + +
659D ASP 3.2 1.8 - - - -
660D SER* 3.0 3.8 + - - -
661D ARG* 3.0 64.4 + - - +
666D GLN 5.6 0.2 - - - -
667D GLY* 4.3 14.4 - - - -
670D GLU* 3.6 29.6 - - + +
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Residues in contact with ILE 658 (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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635D VAL* 5.8 3.8 - - + -
656D SER* 3.7 12.7 - - - +
657D LYS* 1.3 82.5 - - + +
659D ASP* 1.3 57.6 + - - +
661D ARG* 3.4 11.6 + - - +
662D THR* 2.6 42.5 + - - +
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Residues in contact with ASP 659 (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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467D THR* 4.6 4.7 - - - +
633D PRO* 2.8 38.9 - - + +
634D SER* 4.3 6.9 - - - -
654D VAL* 3.8 21.8 - - + -
655D SER* 4.3 8.3 + - - -
656D SER* 3.6 21.0 + - - +
657D LYS 3.2 0.6 - - - -
658D ILE* 1.3 80.3 - - - +
660D SER* 1.3 59.1 + - - +
662D THR* 3.1 2.8 + - - -
663D ILE* 3.0 35.2 + - - +
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Residues in contact with SER 660 (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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654D VAL* 3.9 4.9 - - - +
656D SER 3.9 4.7 + - - -
657D LYS 3.0 11.1 + - - -
659D ASP* 1.3 78.8 - - - +
661D ARG* 1.3 57.2 + - - +
663D ILE* 4.1 2.2 - - - +
664D LEU* 2.9 31.2 + - - +
665D ASP 3.5 2.3 + - - -
666D GLN 4.2 0.5 + - - -
667D GLY* 3.1 7.2 + - - -
668D GLY 3.1 11.4 + - - -
669D ALA* 3.0 35.6 + - - +
670D GLU* 3.3 20.6 - - - -
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Residues in contact with ARG 661 (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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643D LYS* 3.8 0.5 + - - -
657D LYS* 3.0 63.9 + - - +
658D ILE* 3.9 11.3 - - - +
660D SER* 1.3 74.6 - - - +
662D THR* 1.3 63.8 + - - +
665D ASP* 2.7 40.9 + - - +
666D GLN 4.4 10.7 + - - +
667D GLY* 4.4 13.7 - - - +
658E ILE* 6.0 7.0 - - - +
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Residues in contact with THR 662 (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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633D PRO* 3.6 13.4 + - + +
634D SER* 3.6 29.3 - - - -
635D VAL* 3.8 21.8 + - + +
638D ILE* 3.4 31.5 - - + +
643D LYS* 3.5 14.9 - - + +
658D ILE* 2.6 26.8 + - - +
659D ASP* 3.1 10.3 + - - -
661D ARG* 1.3 77.6 - - - +
663D ILE* 1.3 60.6 + - + +
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Residues in contact with ILE 663 (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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463D LEU* 4.9 6.1 - - + +
465D ALA* 3.5 33.4 - - + -
633D PRO* 3.7 12.1 - - + -
638D ILE* 5.1 7.0 - - + -
643D LYS* 4.3 3.1 - - - -
649D ARG* 3.0 48.0 + - + +
650D ILE 4.8 1.8 - - - +
651D ALA* 3.7 16.4 - - + -
654D VAL* 3.6 29.8 - - + -
659D ASP 3.0 14.5 + - - +
660D SER* 4.1 1.6 - - - +
662D THR* 1.3 82.4 - - + +
664D LEU* 1.3 79.2 + - + +
665D ASP 3.8 0.2 + - - -
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Residues in contact with LEU 664 (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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649D ARG* 5.2 3.7 + - + -
650D ILE 5.8 0.2 - - - +
651D ALA* 3.5 35.2 - - + +
660D SER* 2.9 14.6 + - - +
663D ILE* 1.3 84.7 - - + +
665D ASP* 1.3 69.1 + - - +
666D GLN* 3.3 23.7 + - + +
667D GLY 5.1 0.4 - - - +
668D GLY 5.9 0.2 - - - +
669D ALA* 4.6 5.4 - - + +
679D LEU* 3.6 38.8 - - + +
681D LEU* 4.2 34.0 - - + +
688D PRO* 3.7 23.3 - - + -
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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