Contacts of the helix formed by residues 354 - 363 (chain B) in PDB entry 1B70
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 THR 354 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B VAL* 2.7 38.6 + - + +
317B MET* 4.6 14.6 - - + -
352B LEU* 4.8 7.6 - - + -
353B ARG* 1.3 82.5 - - - +
355B GLU* 1.3 66.0 + - - +
356B ALA* 3.3 4.9 + - - +
357B SER* 2.9 22.4 + - - -
358B HIS* 2.9 25.4 + - - +
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Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ALA 5.5 3.3 - - - +
238B GLY 5.7 1.7 - - - +
239B MET* 3.7 31.0 - - + +
253B MET* 3.9 18.2 - - + -
254B LEU* 5.2 3.6 - - - -
354B THR* 1.3 74.6 - - - +
356B ALA* 1.3 60.4 + - - +
358B HIS* 3.7 5.9 + - - +
359B ARG* 2.9 57.8 + - - +
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B MET* 4.3 3.5 - - - -
259B PRO* 3.8 27.6 - - + -
315B GLY 3.7 17.3 - - - +
316B VAL 4.0 7.6 - - - +
354B THR* 3.0 8.8 + - - +
355B GLU* 1.3 76.6 - - - +
357B SER* 1.3 69.0 + - - +
359B ARG* 2.9 14.7 + - - +
360B PHE* 3.0 15.7 + - + -
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLY 3.3 13.8 + - - -
316B VAL* 4.3 18.8 - - - -
343B ILE* 4.0 4.6 - - - +
347B ALA* 4.4 11.9 - - - +
353B ARG* 3.8 10.4 - - - +
354B THR* 2.9 28.5 + - - -
356B ALA* 1.3 78.6 - - - +
358B HIS* 1.3 68.1 + - - +
360B PHE* 3.3 2.1 + - - +
361B GLU* 3.0 37.0 + - - +
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Residues in contact with HIS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 4.3 24.5 - - + +
353B ARG* 3.5 39.0 + - + +
354B THR 2.9 18.4 + - - +
355B GLU* 3.7 8.1 - - - +
357B SER* 1.3 78.2 + - - +
359B ARG* 1.3 70.9 + - - +
361B GLU* 3.4 10.0 + - - +
362B ARG* 3.2 70.1 + - + +
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Residues in contact with ARG 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.2 14.1 - - - +
168B LEU* 2.8 57.7 + - + +
253B MET* 3.7 24.9 + - - -
254B LEU* 3.6 23.9 - - - +
257B ALA* 4.1 20.2 - - + +
259B PRO* 3.9 13.7 - - + -
355B GLU* 2.9 43.2 + - - +
356B ALA 2.9 5.4 + - - +
358B HIS* 1.3 81.8 - - + +
360B PHE* 1.3 57.4 + - - +
362B ARG* 3.1 4.7 + - - +
363B GLY 2.9 32.0 + - - +
364B VAL* 4.6 2.7 - - + -
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Residues in contact with PHE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B PRO* 3.6 36.3 - - + -
315B GLY* 3.2 39.7 - - - -
334B GLU* 4.7 4.5 - - - -
336B ALA 3.3 28.0 - - - -
338B PHE* 3.6 35.2 - + + +
340B PRO* 3.7 17.4 - - - +
343B ILE* 4.3 17.7 - - + -
356B ALA* 3.0 16.8 + - + +
357B SER 3.8 2.9 - - - +
359B ARG* 1.3 77.0 - - - +
361B GLU* 1.3 62.6 + - - +
363B GLY* 3.2 12.5 + - - +
364B VAL* 3.6 27.3 + - + -
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Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 4.3 8.8 - - - -
144A PRO* 4.5 8.1 - - + +
340B PRO* 3.6 20.8 - - - +
343B ILE* 4.4 1.7 - - + +
344B ARG* 3.2 55.5 - - + +
347B ALA* 4.4 5.3 - - - +
348B ARG* 3.9 15.9 + - - +
353B ARG* 5.5 3.3 - - - +
357B SER* 3.0 33.0 + - - +
358B HIS* 3.5 10.4 + - - +
360B PHE* 1.3 79.1 - - - +
362B ARG* 1.3 64.8 + - + +
363B GLY 3.3 0.5 + - - -
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Residues in contact with ARG 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 5.1 6.5 - - - -
144A PRO* 4.0 31.1 - - - +
160B VAL* 3.4 24.9 + - - +
161B THR 4.0 1.2 + - - -
162B PRO* 3.6 36.9 - - + +
165B PRO* 3.6 27.0 - - + +
168B LEU* 4.2 13.9 - - + +
353B ARG* 4.9 4.4 - - - +
358B HIS* 3.2 50.0 + - + +
359B ARG 3.1 5.4 + - - +
361B GLU* 1.3 78.6 - - + +
363B GLY* 1.3 57.5 + - - +
451B LEU* 4.5 2.6 - - - +
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Residues in contact with GLY 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 6.2 0.7 - - - -
165B PRO* 3.3 23.9 - - - +
168B LEU* 5.6 0.5 - - - +
257B ALA* 5.2 2.6 - - - +
340B PRO* 4.9 8.1 - - - -
359B ARG* 2.9 14.4 + - - +
360B PHE 3.2 7.8 + - - -
361B GLU 3.2 4.8 - - - -
362B ARG* 1.3 78.8 - - - +
364B VAL* 1.3 62.6 + - - +
451B LEU* 4.2 13.5 - - - -
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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
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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