Contacts of the helix formed by residues 321 - 332 (chain A) in PDB entry 4J15
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 PHE 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.7 19.7 - - + -
198A LEU* 4.0 18.8 - - + -
201A GLY* 3.6 28.0 - - - -
204A HIS* 6.2 2.2 - - - -
205A LEU* 4.7 6.3 - - + -
316A GLY 4.2 0.4 - - - -
317A LEU* 2.9 37.4 + - + +
320A ARG* 1.3 100.2 - - + +
322A GLN* 1.3 65.8 + - - +
324A GLU* 3.1 38.7 - - + +
325A ILE* 3.0 23.0 + - - +
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Residues in contact with GLN 322 (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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317A LEU 3.8 0.6 + - - -
318A GLN* 3.1 38.2 - - - +
319A GLU 5.1 4.3 - - - +
320A ARG 3.6 2.2 + - - -
321A PHE* 1.3 76.7 - - - +
323A THR* 1.3 63.1 + - - +
325A ILE* 3.2 20.1 + - - +
326A GLN* 2.9 58.8 + - - +
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Residues in contact with THR 323 (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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84A GLN* 4.0 17.0 - - + +
85A PHE* 4.9 18.4 - - + -
322A GLN* 1.3 79.5 - - - +
324A GLU* 1.3 67.6 + - - +
326A GLN* 3.4 7.9 + - - +
327A THR* 2.9 32.0 + - - +
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Residues in contact with GLU 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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84A GLN* 3.6 24.2 + - - +
194A ALA* 3.4 35.7 - - + +
197A ARG* 4.5 8.8 - - - +
198A LEU* 4.3 7.9 - - + +
320A ARG 4.1 2.4 - - - +
321A PHE* 3.1 54.1 - - + +
323A THR* 1.3 82.9 - - - +
325A ILE* 1.3 65.1 + - - +
327A THR* 3.3 0.4 + - - -
328A VAL* 3.1 28.2 + - - +
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Residues in contact with ILE 325 (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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198A LEU* 3.8 18.2 - - + -
317A LEU 3.4 28.0 - - - +
318A GLN* 4.2 10.3 - - + -
321A PHE 3.0 15.8 + - - +
322A GLN* 3.7 22.0 - - - +
324A GLU* 1.3 76.6 - - - +
326A GLN* 1.3 57.7 + - - +
328A VAL* 3.5 1.9 + - - +
329A ASN* 2.9 30.7 + - + +
336A PRO* 6.1 5.6 - - + -
480A PHE* 3.7 27.4 - - + -
481A LEU* 4.3 15.7 - - + +
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Residues in contact with GLN 326 (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 GLN* 2.9 49.2 + - - +
323A THR* 3.7 6.4 - - - +
325A ILE* 1.3 74.3 - - + +
327A THR* 1.3 63.3 + - - +
329A ASN* 3.6 9.8 + - - +
330A LYS* 3.2 27.8 + - - +
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Residues in contact with THR 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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84A GLN* 3.4 13.1 + - + +
190A SER* 3.5 47.6 - - - +
191A THR* 4.0 6.1 + - - +
194A ALA* 3.9 8.1 - - + -
323A THR* 2.9 20.8 + - - +
324A GLU 3.7 4.9 - - - -
325A ILE 3.3 0.4 - - - -
326A GLN* 1.3 76.2 - - - +
328A VAL* 1.3 61.8 + - - +
330A LYS* 3.2 25.6 + - + +
331A GLN* 3.7 3.3 + - - +
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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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191A THR* 4.3 11.0 - - + +
194A ALA* 3.7 17.9 - - + -
195A VAL* 3.9 24.2 - - + +
198A LEU* 6.4 0.4 - - + -
324A GLU 3.1 17.7 + - - +
325A ILE 4.0 2.5 - - - +
327A THR* 1.3 71.5 - - - +
329A ASN* 1.3 61.9 + - - +
331A GLN* 3.1 3.8 + - - +
332A PHE* 2.8 35.7 + - + +
481A LEU* 4.1 28.7 - - + +
483A LEU* 4.0 27.4 - - + -
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Residues in contact with ASN 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 ILE* 2.9 21.3 + - + +
326A GLN* 3.6 10.9 + - - +
327A THR 3.2 0.4 - - - -
328A VAL* 1.3 77.9 - - - +
330A LYS* 1.3 64.4 + - - +
331A GLN 3.3 0.3 + - - -
332A PHE 3.7 5.6 - - - -
333A PRO* 3.3 24.0 - - - +
334A CYS* 2.7 46.0 + - + +
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Residues in contact with LYS 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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160A VAL 5.6 0.2 - - - -
162A PRO* 3.8 16.0 - - - +
326A GLN* 3.2 15.7 + - + +
327A THR* 3.2 17.5 + - + +
329A ASN* 1.3 79.4 - - + +
331A GLN* 1.3 58.2 + - - +
333A PRO* 5.3 2.8 - - - +
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Residues in contact with GLN 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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159A ALA 3.1 20.8 + - - +
160A VAL* 3.3 35.2 - - - +
161A ARG 3.9 6.7 + - - -
162A PRO* 3.9 23.6 - - + +
179A ARG* 4.4 9.2 + - - +
191A THR* 2.7 41.2 + - - +
327A THR 3.7 2.4 + - - +
328A VAL 3.1 3.9 + - - +
330A LYS* 1.3 81.7 - - - +
332A PHE* 1.3 98.6 + - + +
333A PRO* 3.6 8.5 - - - +
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Residues in contact with PHE 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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162A PRO 5.9 2.9 - - - -
179A ARG* 5.8 3.1 - - - -
191A THR* 3.9 11.9 - - + -
328A VAL* 2.8 27.2 + - + +
329A ASN* 3.4 6.1 - - - +
331A GLN* 1.3 118.7 - - + +
333A PRO* 1.3 71.4 - - - +
334A CYS* 3.3 9.0 + - - +
481A LEU 4.5 2.3 - - - +
482A GLY 5.4 4.4 - - - +
483A LEU* 3.5 32.1 - - + -
484A HIS* 6.0 2.5 - + + -
488A GLN* 3.5 30.1 - - + -
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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