Contacts of the helix formed by residues 318 - 331 (chain D) in PDB entry 5ZR1
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 SER 318 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312D GLU* 2.5 44.9 + - - -
315D ASP* 2.9 28.3 + - - -
316D PRO 3.3 1.7 - - - +
317D ARG* 1.3 83.1 - - - +
319D ASN* 1.3 60.9 + - - +
320D LEU 4.3 0.4 - - - -
321D ASN* 3.3 10.9 + - - +
322D ARG* 3.1 26.0 + - - +
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Residues in contact with ASN 319 (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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317D ARG 5.0 2.4 - - - +
318D SER* 1.3 75.2 - - - +
320D LEU* 1.3 64.7 + - - +
322D ARG* 3.4 29.5 + - - +
323D HIS* 3.1 31.2 + - - -
359D LYS 3.3 22.6 + - - +
360D SER* 3.4 30.2 + - - +
361D CYS* 4.2 1.3 - - + -
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Residues in contact with LEU 320 (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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288D VAL* 4.4 11.0 - - + -
292D LEU* 5.3 0.9 - - + -
309D LEU* 4.8 7.6 - - + -
312D GLU* 4.3 15.0 + - + +
313D LEU* 3.7 31.4 - - + -
318D SER* 3.3 1.6 + - - -
319D ASN* 1.3 79.7 - - - +
321D ASN* 1.3 55.4 + - - +
323D HIS* 3.4 2.8 + - + +
324D ILE* 3.2 42.0 + - + +
337D LEU* 6.0 1.6 - - + -
341D ILE* 4.3 21.5 - - + -
358D ILE* 3.8 35.9 - - + +
361D CYS* 3.7 18.0 - - - -
364D LEU* 4.7 5.2 - - + -
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Residues in contact with ASN 321 (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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281D LEU* 5.0 5.4 - - - +
285D VAL* 3.6 27.2 - - - +
312D GLU 4.2 3.8 - - - +
313D LEU* 3.7 20.2 + - + -
315D ASP 3.7 15.3 + - - +
316D PRO* 3.7 20.3 + - - +
318D SER* 3.3 21.2 + - - +
319D ASN 3.3 0.4 - - - -
320D LEU* 1.3 76.6 - - - +
322D ARG* 1.3 61.7 + - - +
324D ILE* 3.9 10.2 - - - +
325D ARG* 3.4 30.0 + - - +
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Residues in contact with ARG 322 (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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853A GLY 4.6 3.8 - - - -
854A SER* 4.6 16.0 - - - -
316D PRO 5.7 0.7 - - - +
317D ARG 5.9 0.2 - - - -
318D SER 3.1 13.4 + - - +
319D ASN* 3.5 35.1 + - - +
320D LEU 3.2 0.4 - - - -
321D ASN* 1.3 77.2 - - - +
323D HIS* 1.3 88.0 + - - +
324D ILE 3.2 0.2 - - - -
325D ARG* 3.3 13.6 + - - +
326D MET* 3.2 54.1 + - + +
360D SER 4.8 3.0 + - - -
361D CYS 5.2 0.2 + - - -
365D ASP* 4.3 9.9 + - - -
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Residues in contact with HIS 323 (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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852A GLN 6.0 0.9 - - - -
319D ASN 3.1 23.5 + - - -
320D LEU* 3.4 7.6 + - + +
322D ARG* 1.3 100.0 + - - +
324D ILE* 1.3 64.7 + - - +
326D MET* 3.7 17.6 + - + +
327D ASN* 3.4 19.8 + - - +
337D LEU* 4.3 11.5 - - + +
361D CYS* 3.6 29.2 + - + -
364D LEU* 3.7 36.2 - - + +
365D ASP* 3.1 25.7 + - - -
368D ASN* 4.2 10.5 + - - -
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Residues in contact with ILE 324 (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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281D LEU* 4.3 10.3 - - + -
284D MET* 3.8 39.1 - - + +
285D VAL* 4.3 6.7 - - + -
288D VAL* 4.1 17.3 - - + -
313D LEU* 3.9 16.4 - - + -
320D LEU* 3.2 41.0 + - + +
321D ASN* 4.0 11.2 - - - +
322D ARG 3.2 0.4 - - - -
323D HIS* 1.3 76.3 - - - +
325D ARG* 1.3 58.8 + - - +
327D ASN* 3.2 4.0 + - - +
328D PHE* 3.1 26.0 + - - +
337D LEU* 3.9 20.9 - - + -
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Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D LEU* 3.4 39.6 - - + +
316D PRO* 4.0 28.6 + - - +
321D ASN* 3.4 24.5 + - - +
322D ARG* 3.3 13.6 + - - +
324D ILE* 1.3 80.1 - - - +
326D MET* 1.3 60.8 + - + +
328D PHE* 3.3 2.1 + - - +
329D GLU* 3.2 36.7 + - + +
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Residues in contact with MET 326 (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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848A THR* 4.2 28.0 - - + +
852A GLN* 4.3 23.1 - - + +
853A GLY* 3.6 27.6 - - - -
322D ARG* 3.2 59.2 + - + +
323D HIS* 4.1 21.3 - - + +
325D ARG* 1.3 73.8 - - + +
327D ASN* 1.3 58.3 + - - +
329D GLU* 3.5 4.2 + - - +
330D THR* 2.6 40.0 + - + +
368D ASN* 5.7 1.6 - - - -
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Residues in contact with ASN 327 (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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284D MET* 3.4 16.0 - - + +
323D HIS 3.4 11.3 + - - +
324D ILE* 3.2 11.3 + - - +
326D MET* 1.3 78.9 - - - +
328D PHE* 1.3 54.6 + - - +
330D THR* 3.9 2.9 - - - -
331D PHE* 3.0 36.6 + - - +
332D ARG* 2.5 33.1 + - - -
333D SER 2.9 25.0 + - - +
336D THR* 4.5 2.9 - - - +
337D LEU* 3.3 32.2 - - + +
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Residues in contact with PHE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A SER* 4.4 1.2 + - - -
278D ILE* 3.7 10.3 - - + -
279D GLN 3.7 9.6 - - - -
280D ASN* 3.2 37.2 - - - -
281D LEU* 3.7 29.2 - - + -
284D MET* 3.8 21.7 - - - -
324D ILE 3.1 12.2 + - - +
325D ARG* 3.6 8.3 - - + +
326D MET 3.3 0.4 - - - -
327D ASN* 1.3 77.6 - - - +
329D GLU* 1.3 82.1 + - - +
332D ARG* 3.2 65.5 + - + +
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Residues in contact with GLU 329 (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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798A SER* 3.6 0.9 - - - -
799A PHE* 3.3 35.3 + - - +
800A THR* 3.3 11.4 + - - -
841A PHE* 3.6 27.2 - - - -
845A ILE* 3.9 22.4 - - + +
848A THR* 5.6 2.5 - - - +
849A LEU* 6.0 0.2 - - - +
325D ARG* 3.2 28.3 + - + +
326D MET* 4.2 4.7 - - - +
327D ASN 3.2 0.4 - - - -
328D PHE* 1.3 104.0 - - - +
330D THR* 1.3 64.1 + - + +
332D ARG* 5.3 2.1 + - - -
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Residues in contact with THR 330 (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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798A SER* 3.2 16.3 + - - -
800A THR* 3.4 17.1 - - - +
845A ILE* 6.2 0.7 - - + -
848A THR* 3.9 21.8 - - - +
849A LEU* 5.1 7.4 - - + -
852A GLN* 5.2 3.0 + - + -
864A ILE* 4.1 17.1 - - + +
865A SER* 2.9 23.8 + - - -
869A VAL* 3.9 4.9 - - - +
326D MET* 2.6 24.7 + - + +
329D GLU* 1.3 84.8 - - + +
331D PHE* 1.3 83.8 + - - +
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Residues in contact with PHE 331 (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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798A SER* 3.1 9.6 + - - -
852A GLN* 4.2 20.0 - - - -
864A ILE* 4.2 6.3 - - + -
865A SER* 3.5 26.9 - - - -
867A ASP* 5.5 1.6 - - - -
868A PHE* 3.5 52.3 - + + -
872A GLN* 4.7 5.7 + - - +
327D ASN* 3.0 21.8 + - - +
330D THR* 1.3 103.8 + - - +
332D ARG* 1.3 69.3 + - - +
333D SER* 3.3 11.7 - - - +
336D THR* 4.1 23.8 - - + -
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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