Contacts of the helix formed by residues 316 - 331 (chain P) 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 ARG 316 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314P LEU* 4.8 12.3 - - + +
315P MET* 1.3 93.0 - - - +
317P TRP* 1.3 67.8 - - - +
318P SER* 3.4 19.3 + - - +
319P THR* 3.7 22.9 + - - +
320P LEU* 3.7 6.8 + - - +
362P ASN* 4.0 5.7 - - - +
380P GLN* 4.1 12.9 + - - +
381P LEU* 4.8 8.9 + - - +
383P ASP* 3.0 31.3 + - - +
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Residues in contact with TRP 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315P MET* 5.4 0.4 - - + -
316P ARG* 1.3 72.2 - - - +
318P SER* 1.3 69.1 + - - +
320P LEU* 2.9 43.0 + - + -
321P VAL* 3.0 18.2 + - + +
328P LEU* 5.7 0.9 - - + -
351P TRP* 2.5 51.8 - + - -
354P LEU* 3.0 21.3 - - + -
355P LYS* 4.5 24.5 - - + +
358P VAL* 4.1 32.1 - - + +
383P ASP* 3.8 19.2 + - + +
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Residues in contact with SER 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316P ARG* 3.4 20.7 + - - -
317P TRP* 1.3 77.8 + - - +
319P THR* 1.3 64.9 + - - +
321P VAL* 3.1 10.1 + - - +
322P GLU* 2.9 25.1 + - - +
383P ASP* 5.1 5.0 + - - +
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Residues in contact with THR 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315P MET 5.0 1.6 - - - -
316P ARG* 3.7 24.1 + - - +
317P TRP 3.3 0.6 - - - -
318P SER* 1.3 78.3 - - - +
320P LEU* 1.3 63.2 + - - +
322P GLU* 3.4 7.1 + - - +
323P ASP* 2.9 28.3 + - - +
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Residues in contact with LEU 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305P LEU* 5.5 5.6 - - + -
308P LEU* 5.0 4.5 - - + -
309P PHE* 6.4 0.4 - - + -
315P MET* 4.7 19.3 - - + +
316P ARG 3.7 6.7 + - - +
317P TRP* 2.9 38.9 + - + +
319P THR* 1.3 79.1 - - - +
321P VAL* 1.3 63.8 + - - +
323P ASP* 2.9 24.4 - - - -
324P TYR* 2.9 28.8 + - + +
328P LEU* 5.9 2.9 - - + -
354P LEU* 5.3 3.6 - - + -
358P VAL* 5.7 0.2 - - + -
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Residues in contact with VAL 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317P TRP* 3.0 58.0 + - + +
318P SER* 3.5 8.7 - - - +
320P LEU* 1.3 78.2 - - - +
322P GLU* 1.3 58.8 + - - +
325P GLY* 2.7 38.0 + - - +
328P LEU* 6.0 2.0 - - - -
351P TRP* 3.5 20.9 - - + -
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Residues in contact with GLU 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318P SER 2.9 16.4 + - - +
319P THR* 3.6 7.9 - - - +
321P VAL* 1.3 82.3 - - - +
323P ASP* 1.3 68.0 + - + +
325P GLY* 3.8 3.1 + - - -
326P MET* 4.8 6.1 - - - +
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Residues in contact with ASP 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301P LYS* 5.5 0.2 - - - +
319P THR 2.9 21.4 + - - +
320P LEU* 2.9 19.5 - - - -
322P GLU* 1.3 79.5 - - + +
324P TYR* 1.3 103.7 + - + +
326P MET* 4.5 8.0 - - - +
327P GLU* 5.4 2.8 + - - +
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Residues in contact with TYR 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301P LYS* 2.6 46.2 - - + -
304P ASP* 2.0 47.9 - - + +
305P LEU* 4.1 20.6 - - + -
308P LEU* 4.3 21.5 - - + +
320P LEU* 2.9 20.0 + - + +
323P ASP* 1.3 106.6 - - + +
325P GLY* 1.4 62.7 + - - +
326P MET 3.4 2.2 - - - -
327P GLU* 3.1 6.5 + - + +
328P LEU* 3.0 40.0 + - + +
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Residues in contact with GLY 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321P VAL* 2.7 32.0 + - - -
322P GLU 3.8 1.3 + - - -
323P ASP 3.6 1.4 - - - -
324P TYR* 1.4 67.8 - - - +
326P MET* 1.3 62.5 + - - +
328P LEU* 3.5 9.5 + - - +
329P ARG* 3.0 31.3 + - - +
351P TRP* 5.9 3.4 - - - -
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Residues in contact with MET 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322P GLU 4.8 4.9 - - - +
323P ASP 4.5 11.9 - - - +
325P GLY* 1.3 74.7 - - - +
327P GLU* 1.3 57.1 + - + +
329P ARG* 3.4 2.8 - - - +
330P LYS* 2.4 44.3 + - + +
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Residues in contact with GLU 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301P LYS* 4.4 28.9 - - + -
302P TYR* 5.9 5.4 - - + -
323P ASP 5.6 2.2 - - - +
324P TYR* 3.1 9.3 + - + +
326P MET* 1.3 78.7 - - + +
328P LEU* 1.3 65.8 + - - +
330P LYS* 3.6 8.7 - - + +
331P GLY* 3.3 14.4 + - - -
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Residues in contact with LEU 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272P LEU* 4.9 14.1 - - + -
305P LEU* 5.2 12.8 - - + -
317P TRP* 5.7 1.1 - - + -
320P LEU* 5.7 3.8 - - + +
321P VAL* 6.0 1.3 - - - -
324P TYR* 3.0 37.2 + - + +
325P GLY* 3.6 7.4 - - - +
327P GLU* 1.3 79.9 - - - +
329P ARG* 1.3 64.8 + - + +
331P GLY* 3.0 11.4 + - - -
341P PHE* 3.6 54.3 + - + +
351P TRP* 5.2 8.1 - - + -
354P LEU* 4.6 13.0 - - + -
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Residues in contact with ARG 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325P GLY* 3.0 18.5 + - - +
326P MET* 3.9 2.9 - - - +
328P LEU* 1.3 79.8 - - + +
330P LYS* 1.3 64.2 + - - +
331P GLY 3.1 9.4 + - - +
341P PHE* 5.2 19.4 - - + +
351P TRP* 6.1 3.4 - - - +
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Residues in contact with LYS 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P MET* 2.4 37.8 + - + +
327P GLU* 3.6 10.8 - - + +
329P ARG* 1.3 68.4 - - - +
331P GLY* 1.3 65.8 + - - +
332P SER* 3.5 1.7 + - - -
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Residues in contact with GLY 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327P GLU 3.3 5.9 + - - -
328P LEU 3.0 15.4 + - - -
329P ARG 3.1 8.8 - - - +
330P LYS* 1.3 86.2 - - - +
332P SER* 1.3 63.7 + - - +
341P PHE 5.3 5.5 - - - +
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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
------------------------------------------------------------
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