Contacts of the helix formed by residues 323 - 334 (chain A) in PDB entry 1ZVR
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 PRO 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ARG* 1.4 82.2 - - + +
324A SER* 1.3 65.8 + - - +
325A VAL* 3.4 10.1 - - + +
326A ASN* 3.1 36.4 + - - +
327A ALA* 3.0 19.1 + - - +
350A PHE* 4.5 0.2 - - - -
352A ASP* 3.4 35.9 - - + +
353A ILE 3.5 12.3 - - - +
354A HIS* 3.8 24.0 - - + +
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Residues in contact with SER 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG 3.6 0.8 + - - -
323A PRO* 1.3 70.1 - - - +
325A VAL* 1.3 70.1 + - - +
327A ALA* 3.0 6.4 + - - +
328A VAL* 3.0 30.2 + - - +
350A PHE* 3.7 34.5 - - - -
352A ASP* 3.9 6.3 + - - -
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO* 4.6 8.5 - - + -
324A SER* 1.3 80.9 - - - +
326A ASN* 1.3 71.7 + - - +
328A VAL* 3.4 8.1 + - - +
329A ALA* 2.9 28.6 + - - +
354A HIS* 6.2 2.0 - - + -
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Residues in contact with ASN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 4.3 9.4 - - + -
323A PRO* 3.1 38.1 + - + +
325A VAL* 1.3 87.4 - - - +
327A ALA* 1.3 66.0 + - - +
329A ALA* 3.1 7.0 + - - +
330A ASN* 2.8 35.1 + - - +
354A HIS* 4.1 13.5 + - - -
355A ASN* 4.6 8.7 - - - +
423A ARG* 4.5 8.1 - - - +
3632A 3PI 4.5 14.6 + - - +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ASP* 4.1 0.2 - - - +
322A ARG* 3.8 28.2 - - - +
323A PRO 3.0 8.4 + - - +
324A SER 3.0 7.7 + - - +
326A ASN* 1.3 78.2 - - - +
328A VAL* 1.3 59.8 + - - +
330A ASN* 3.4 4.3 + - - +
331A LYS* 3.1 19.6 + - - +
336A GLY* 3.9 6.8 - - - -
337A TYR* 4.1 8.4 - - + -
350A PHE* 3.3 37.2 - - + -
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A SER* 3.0 20.2 + - - +
325A VAL* 3.8 8.7 - - - +
327A ALA* 1.3 75.1 - - - +
329A ALA* 1.3 65.8 + - - +
330A ASN 3.1 0.2 - - - -
331A LYS* 3.0 22.0 + - + +
332A ALA* 3.1 12.4 + - + +
337A TYR* 4.4 18.8 - - + +
350A PHE* 6.0 0.9 - - + -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A VAL 2.9 18.4 + - - +
326A ASN* 3.5 9.9 - - - +
328A VAL* 1.3 76.8 - - - +
330A ASN* 1.4 63.1 + - - +
332A ALA* 3.2 21.7 + - - +
333A LYS* 3.4 7.8 + - - +
3632A 3PI 5.8 4.4 - - + +
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Residues in contact with ASN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A GLN* 3.3 20.6 + - - +
322A ARG* 3.2 21.4 - - - +
326A ASN* 2.8 26.9 + - - +
327A ALA 3.4 5.6 - - - +
329A ALA* 1.4 76.5 - - - +
331A LYS* 1.3 59.5 + - - +
333A LYS* 3.1 5.2 + - - +
334A GLY 2.8 11.1 + - - -
335A GLY* 2.8 21.1 + - - -
336A GLY 3.9 0.4 - - - -
418A SER* 3.2 9.2 + - - -
3632A 3PI 3.0 62.3 + - - +
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A VAL* 3.9 15.8 - - + +
290A GLY 3.2 25.9 - - - +
291A VAL* 3.0 33.3 + - - +
293A GLY* 5.2 5.0 - - - +
327A ALA 3.1 9.0 + - - +
328A VAL* 3.0 17.1 + - + +
330A ASN* 1.3 77.6 - - - +
332A ALA* 1.3 61.9 - - - +
334A GLY 3.3 4.7 + - - -
335A GLY 3.5 13.9 - - - +
336A GLY* 3.7 12.5 - - - +
337A TYR* 4.4 26.9 + - + +
339A SER* 6.2 2.2 - - - -
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A VAL* 2.9 30.1 - - + +
328A VAL* 3.1 11.2 + - + +
329A ALA* 3.3 13.9 - - - +
330A ASN 3.2 0.2 - - - -
331A LYS* 1.3 76.6 - - - +
333A LYS* 1.3 59.6 - - - +
334A GLY* 4.7 0.2 - - - -
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Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ALA 3.4 7.5 + - - +
330A ASN* 3.1 3.7 + - - +
332A ALA* 1.3 79.8 - - - +
334A GLY* 1.3 55.3 + - - +
3632A 3PI 3.4 78.8 + - + +
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A MET* 3.4 28.6 - - - +
290A GLY* 3.3 23.3 + - - -
330A ASN 2.8 1.0 + - - -
331A LYS 3.3 3.8 + - - -
332A ALA 3.4 0.6 - - - -
333A LYS* 1.3 80.4 - - - +
335A GLY* 1.3 68.1 + - - +
3632A 3PI 4.2 4.0 - - - -
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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