Contacts of the helix formed by residues 326 - 335 (chain A) in PDB entry 5HLB
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 GLY 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A MET 3.4 13.7 - - - -
312A ASN* 3.4 16.9 + - - -
313A GLU 4.3 0.2 - - - -
314A VAL* 2.8 18.2 + - - -
316A LEU* 3.9 6.0 - - - +
325A ARG* 1.3 76.3 - - - +
327A PHE* 1.3 65.0 + - - -
328A PRO* 3.4 5.5 - - - -
329A LEU 3.6 1.0 + - - -
330A ALA* 3.2 19.4 + - - +
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Residues in contact with PHE 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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221A PHE* 4.0 9.4 - - + -
225A LEU* 4.4 9.4 - - + -
229A LEU* 4.4 16.6 - - + -
310A TYR* 4.8 2.0 - + - -
311A MET* 3.1 47.0 + - + -
314A VAL* 3.7 21.5 - - + -
316A LEU* 3.7 17.4 - - + +
326A GLY* 1.3 70.8 - - - -
328A PRO* 1.4 63.1 - - + +
330A ALA* 3.1 1.5 + - - -
331A SER* 2.9 35.9 + - - -
339A VAL* 4.1 10.1 - - + -
350A LEU* 3.8 42.3 - - + +
351A VAL* 3.9 22.9 - - + -
354A VAL* 5.4 4.0 - - + -
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Residues in contact with PRO 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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214A LEU* 3.2 31.0 - - + +
216A VAL* 3.6 28.3 - - + -
221A PHE* 3.6 9.6 - - + -
311A MET 3.6 10.8 - - - +
312A ASN* 3.5 14.8 - - - +
326A GLY* 3.4 6.3 - - - -
327A PHE* 1.4 93.0 - - + +
329A LEU* 1.3 60.1 + - - +
331A SER* 3.7 5.9 + - - -
332A LEU* 3.5 23.1 + - - +
338A PRO* 5.0 0.5 - - - +
339A VAL* 4.2 15.8 + - + +
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Residues in contact with LEU 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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201A LEU* 4.9 3.6 - - + -
204A MET* 3.8 35.7 - - + -
212A GLN* 3.6 43.5 - - + +
213A ARG 4.0 1.3 - - - +
214A LEU* 4.0 28.0 + - + +
324A ILE* 4.0 22.2 - - + -
325A ARG 4.3 9.2 + - - +
326A GLY 3.6 1.6 + - - -
327A PHE 3.4 0.4 - - - -
328A PRO* 1.3 76.8 - - - +
330A ALA* 1.4 58.5 + - - +
332A LEU* 3.6 12.5 + - + +
333A TYR* 3.0 30.5 + - + +
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Residues in contact with ALA 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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316A LEU* 3.7 31.6 - - + -
324A ILE* 4.2 7.1 - - + +
326A GLY 3.2 18.1 + - - +
327A PHE* 3.1 6.0 + - - +
329A LEU* 1.4 73.7 - - - +
331A SER* 1.4 57.2 + - - +
333A TYR* 3.2 6.9 + - - -
334A TYR* 3.0 45.4 + - + +
350A LEU* 4.2 10.3 - - + +
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Residues in contact with SER 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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327A PHE 2.9 19.3 + - - -
328A PRO 3.9 2.0 - - - -
329A LEU 3.5 0.2 - - - -
330A ALA* 1.4 74.8 - - - +
332A LEU* 1.4 52.8 + - - +
335A PHE* 2.8 37.0 + - - +
336A GLY 3.0 4.7 + - - -
337A ARG 3.2 18.3 - - - +
339A VAL* 3.4 23.3 - - - +
342A LEU* 3.3 30.9 - - - +
350A LEU* 3.4 8.9 - - - +
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Residues in contact with LEU 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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132A GLN* 5.3 7.8 + - + +
201A LEU* 4.1 27.6 - - + -
214A LEU* 3.7 27.1 - - + -
328A PRO 3.5 17.7 + - - +
329A LEU* 3.6 11.6 + - + +
330A ALA 3.3 0.4 - - - -
331A SER* 1.4 75.0 - - - +
333A TYR* 1.4 62.2 + - - +
336A GLY* 3.0 28.7 + - - +
337A ARG* 3.7 25.1 - - - +
338A PRO* 3.7 14.6 - - + -
403A PRO* 5.2 1.7 - - - +
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Residues in contact with TYR 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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318A GLN 2.8 27.8 + - - -
319A SER* 3.6 17.2 - - - -
324A ILE* 4.2 24.7 - - + -
329A LEU* 3.0 20.2 + - + +
330A ALA* 3.2 8.2 + - - +
332A LEU* 1.4 77.5 - - - +
334A TYR* 1.3 92.6 + + - +
363A TRP* 4.3 19.5 + + - -
403A PRO* 4.1 13.2 - - - +
406A GLY 3.4 18.9 + - - -
407A VAL* 4.0 35.7 - - + +
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Residues in contact with TYR 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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316A LEU* 2.8 30.5 + - + -
317A GLY* 3.2 15.4 - - - -
318A GLN 4.4 0.3 + - - -
324A ILE* 5.3 0.9 - - + -
330A ALA* 3.0 34.6 + - + +
333A TYR* 1.3 95.6 - + - +
335A PHE* 1.3 77.6 + + + +
349A LEU* 5.9 0.9 - - + -
350A LEU* 4.4 10.1 - - + -
353A MET* 3.6 15.0 - - + +
361A ASN* 4.3 9.1 + - - -
362A PRO* 4.0 21.1 - - + -
363A TRP* 3.9 24.9 - + - -
401A VAL 2.9 14.9 - - - +
402A GLN* 3.1 27.2 + - - +
403A PRO* 3.1 16.7 - - - +
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Residues in contact with PHE 335 (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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331A SER* 2.8 19.7 + - - +
334A TYR* 1.3 79.5 - - + +
336A GLY* 1.3 57.3 + - - +
337A ARG* 3.5 22.5 - - + +
342A LEU* 4.0 12.1 - - + -
346A GLN* 3.6 44.6 - - + +
349A LEU* 3.3 27.1 - - + -
350A LEU* 3.6 29.2 - - + -
399A LEU 3.2 24.2 - - - -
401A VAL* 3.3 28.2 - - + +
402A GLN* 3.3 14.6 - - - -
403A PRO* 5.1 5.1 - - - +
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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