Contacts of the helix formed by residues 686 - 693 (chain f) in PDB entry 5T0J
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 ARG 686 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317f THR* 5.0 17.9 - - + +
353f MET* 4.6 9.3 - - - +
354f GLU* 4.2 20.6 + - - -
394f THR* 3.0 42.4 + - - +
397f ARG* 4.9 11.4 - - - +
429f ARG* 4.1 29.0 - - - +
685f VAL* 1.3 87.1 - - + +
687f VAL* 1.3 67.0 + - + +
688f GLY 3.1 7.1 + - - -
689f GLN* 3.4 14.7 + - - +
690f ALA* 3.6 10.7 + - - +
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Residues in contact with VAL 687 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397f ARG* 4.5 16.8 - - - +
429f ARG* 5.3 8.3 - - - +
679f ARG* 4.1 31.4 - - + +
680f PRO* 4.5 3.6 - - + +
682f PRO 4.6 3.1 - - - +
683f VAL* 3.6 20.6 - - + -
684f SER* 3.6 31.6 - - - +
685f VAL* 4.5 2.5 - - + +
686f ARG* 1.3 84.2 - - + +
688f GLY* 1.3 62.6 + - - +
689f GLN 3.5 0.2 - - - -
690f ALA* 3.8 9.5 + - - +
691f VAL* 3.4 23.2 + - - +
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Residues in contact with GLY 688 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287f LEU* 4.3 9.0 - - - -
648f ARG* 4.6 6.1 + - - -
680f PRO* 5.5 4.3 - - - -
683f VAL* 5.1 6.2 - - - +
685f VAL 4.2 6.0 + - - -
686f ARG* 3.1 1.8 - - - +
687f VAL* 1.3 81.8 - - - +
689f GLN* 1.3 62.8 + - - +
691f VAL* 3.4 9.5 + - - +
692f ASP* 3.3 16.5 + - - +
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Residues in contact with GLN 689 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286f LEU 3.0 18.7 + - - +
287f LEU* 3.2 44.0 + - + +
290f GLY 5.8 0.4 - - - +
317f THR* 2.8 49.5 + - + +
318f MET* 3.4 13.9 + - - +
320f LEU* 3.3 29.5 - - + +
321f GLY 4.6 2.6 - - - +
685f VAL 5.3 0.4 + - - -
686f ARG* 3.4 10.6 + - + +
688f GLY* 1.3 74.9 - - - +
690f ALA* 1.3 66.4 + - - +
692f ASP* 3.0 20.1 + - + +
693f VAL* 3.7 1.7 + - - +
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Residues in contact with ALA 690 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320f LEU* 4.1 7.1 - - + +
397f ARG* 6.2 0.9 - - - +
398f TRP* 3.1 43.3 - - + +
676f GLU* 3.2 23.4 - - - +
679f ARG* 4.9 5.6 - - - -
686f ARG 3.6 10.3 + - - +
687f VAL* 3.9 13.0 - - - +
688f GLY 3.3 0.8 - - - -
689f GLN* 1.3 78.7 - - - +
691f VAL* 1.3 59.6 + - + +
693f VAL* 3.5 5.4 + - - +
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Residues in contact with VAL 691 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648f ARG* 5.1 3.3 + - - +
676f GLU* 3.3 39.7 - - + +
677f GLU* 3.3 32.8 - - + +
679f ARG* 5.1 0.4 - - + -
680f PRO* 3.6 16.4 - - + -
687f VAL 3.4 17.9 - - - +
688f GLY* 3.4 7.5 + - - +
689f GLN 3.2 0.2 - - - -
690f ALA* 1.3 73.6 - - - +
692f ASP* 1.3 62.1 + - - +
693f VAL 3.1 6.8 + - - -
694f VAL* 3.3 21.0 + - + +
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Residues in contact with ASP 692 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287f LEU* 3.1 19.2 - - + +
288f ALA* 3.3 20.5 - - - +
291f ILE* 3.5 34.9 + - - +
321f GLY* 5.3 4.0 + - - -
648f ARG* 3.2 38.0 + - - +
651f ILE* 4.3 1.9 - - - +
688f GLY 3.3 4.2 + - - -
689f GLN* 3.0 27.3 + - + +
691f VAL* 1.3 75.3 - - - +
693f VAL* 1.3 62.5 + - - +
694f VAL* 3.2 5.4 + - - -
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Residues in contact with VAL 693 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291f ILE* 3.3 23.9 - - + +
320f LEU* 3.8 35.4 - - + -
321f GLY* 5.5 1.3 - - - +
324f PHE* 4.1 26.6 - - + -
361f LEU* 5.0 2.5 - - + -
365f MET* 3.7 36.2 - - + +
398f TRP* 3.7 15.9 - - + -
690f ALA 3.5 17.5 - - - +
691f VAL 3.1 0.6 - - - -
692f ASP* 1.3 78.4 - - - +
694f VAL* 1.3 62.5 + - + +
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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