Contacts of the helix formed by residues 359 - 370 (chain I) in PDB entry 5GJQ
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 359 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357I ASP* 2.8 15.2 + - - +
358I GLU* 1.3 83.7 - - + +
360I THR* 1.3 70.3 + - + +
361I LYS 3.1 0.4 - - - -
362I LYS* 2.7 29.8 + - + +
363I ARG* 3.1 7.9 + - - +
198k VAL 5.2 1.2 + - - -
199k VAL 3.4 8.2 + - - -
200k GLN* 3.2 42.0 - - - +
201k SER* 3.6 18.6 - - - +
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Residues in contact with THR 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I GLY* 3.0 41.5 - - - +
190I LEU 4.4 1.1 - - - +
356I PRO* 3.0 19.7 - - + +
357I ASP* 2.8 25.0 + - - +
359I LYS* 1.3 76.2 - - + +
361I LYS* 1.3 59.7 + - - +
363I ARG* 2.8 10.5 + - - +
364I ILE* 2.8 40.7 + - - +
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Residues in contact with LYS 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I LEU 5.0 0.9 - - - -
356I PRO* 2.8 32.5 - - + -
357I ASP* 3.5 27.0 + - - +
358I GLU 4.4 3.6 - - - -
359I LYS 3.1 0.2 - - - -
360I THR* 1.3 81.2 + - - +
362I LYS* 1.3 53.7 + - - +
364I ILE* 2.9 10.1 + - - +
365I PHE* 2.4 39.7 + - - +
384I ILE* 3.8 36.2 + - + +
387I LYS 4.9 1.0 + - - -
388I ASP 4.6 5.1 + - - -
389I ASP* 4.1 6.6 - - - +
390I LEU* 2.9 52.5 + - + +
395I ILE* 3.7 16.1 - - + +
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Residues in contact with LYS 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I GLU* 2.9 35.4 + - - +
359I LYS* 2.7 24.1 + - + +
361I LYS* 1.3 74.3 - - - +
363I ARG* 1.3 51.9 + - + +
365I PHE* 3.9 1.2 - - - +
366I GLN* 2.8 37.5 + - - +
380I LEU* 4.7 2.9 - - + +
381I ASP* 3.2 28.8 + - - +
384I ILE* 3.1 21.3 - - + +
201k SER* 5.2 5.9 + - - -
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Residues in contact with ARG 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ILE 5.9 0.4 + - - -
188I GLY* 3.5 13.4 - - - -
189I GLY* 3.9 17.3 - - - +
191I ASP* 3.7 31.6 + - - -
359I LYS 3.1 8.8 + - - +
360I THR* 2.8 11.3 + - - +
362I LYS* 1.3 77.6 - - + +
364I ILE* 1.3 56.1 + - - +
366I GLN* 4.5 8.7 - - - +
367I ILE* 2.3 48.3 + - + +
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Residues in contact with ILE 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I GLY* 2.7 29.8 - - - +
356I PRO* 3.5 28.9 - - + -
360I THR* 2.8 25.2 + - - +
361I LYS* 3.3 7.4 - - + +
363I ARG* 1.3 76.0 - - - +
365I PHE* 1.3 59.8 + - - +
367I ILE* 3.4 5.6 + - - -
368I HIS* 2.9 43.2 + - + +
392I GLY* 3.9 23.1 - - - +
395I ILE* 4.3 10.1 - - + -
501I ADP 3.4 33.0 - - + +
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Residues in contact with PHE 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361I LYS 2.4 29.9 + - - +
362I LYS* 3.9 3.6 - - - +
364I ILE* 1.3 66.3 - - - +
366I GLN* 1.3 57.9 + - - +
368I HIS* 3.0 1.9 + - - -
369I THR* 2.7 42.2 + - + +
380I LEU* 3.2 39.9 - - + -
383I LEU* 2.7 53.8 - - + -
384I ILE* 3.6 14.6 - - + -
390I LEU* 6.1 0.4 - - + -
395I ILE* 2.1 63.0 - - + -
398I ILE* 4.6 8.5 - - + -
399I CYS* 5.0 5.2 - - - -
419I PHE* 5.5 0.2 - + - -
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Residues in contact with GLN 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362I LYS 2.8 21.2 + - - +
363I ARG* 3.8 7.1 - - - +
365I PHE* 1.3 72.9 - - - +
367I ILE* 1.3 75.7 + - - +
369I THR* 3.8 0.4 - - - -
370I SER* 2.4 51.2 + - - -
380I LEU* 3.3 19.4 - - + +
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Residues in contact with ILE 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ALA 5.5 2.2 - - - +
186I ASP* 3.7 35.9 - - - +
188I GLY* 3.3 30.5 - - - +
363I ARG* 2.3 45.4 + - + +
364I ILE* 3.7 4.7 - - - +
366I GLN* 1.3 91.1 - - - +
368I HIS* 1.3 66.7 + - + +
370I SER* 3.2 16.8 + - - -
371I ARG* 4.1 24.4 - - - +
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Residues in contact with HIS 368 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I ASP* 4.7 7.0 + - - -
364I ILE* 2.9 24.5 + - + +
365I PHE* 3.0 3.1 + - + +
367I ILE* 1.3 91.8 - - + +
369I THR* 1.3 59.9 + - - +
370I SER 3.4 0.4 + - - -
371I ARG* 4.3 5.3 + - - +
372I MET* 4.1 8.8 - - - +
392I GLY 4.0 5.8 - - - -
395I ILE* 4.8 0.6 - - - +
396I LYS* 3.3 40.5 + - + +
399I CYS* 3.3 26.2 - - + +
501I ADP 3.5 43.0 + + - -
179J GLY 4.8 4.9 - - - +
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Residues in contact with THR 369 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365I PHE* 2.7 26.0 + - + +
366I GLN* 3.8 0.5 - - - -
368I HIS* 1.3 71.3 - - - +
370I SER* 1.3 63.3 + - - +
371I ARG 3.3 2.2 - - - -
372I MET* 3.6 14.2 - - - +
374I LEU* 2.5 52.6 - - + +
380I LEU* 3.1 34.0 - - + +
399I CYS* 2.8 30.1 - - - -
419I PHE* 3.8 8.1 - - + -
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Residues in contact with SER 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366I GLN* 2.4 37.7 + - - -
367I ILE* 3.2 15.4 + - - -
369I THR* 1.3 78.0 - - - +
371I ARG* 1.3 64.1 + - - +
372I MET 3.3 7.4 + - - +
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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