Contacts of the helix formed by residues 377 - 389 (chain A) in PDB entry 2IBS
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 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A GLN 3.0 13.7 + - - -
374A TRP* 2.7 42.1 + - - -
376A ASN* 1.3 83.3 - - - +
378A GLU* 1.3 63.7 + - - +
379A ALA* 3.8 3.8 + - - -
380A MET* 3.3 15.6 + - - +
381A GLN* 3.2 15.5 + - - +
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Residues in contact with GLU 378 (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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340A ARG* 5.8 1.6 + - - -
376A ASN 4.1 9.7 - - - +
377A SER* 1.3 72.3 - - - +
379A ALA* 1.3 64.8 + - - +
380A MET 3.3 0.2 - - - -
381A GLN* 3.8 17.3 - - - +
382A LYS* 3.1 25.5 + - - +
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Residues in contact with ALA 379 (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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253A LEU* 4.5 6.9 - - + +
374A TRP* 4.0 26.2 - - + -
377A SER* 4.0 3.1 - - - +
378A GLU* 1.3 79.8 - - - +
380A MET* 1.3 56.5 + - - +
382A LYS* 3.9 6.5 - - - +
383A HIS* 3.1 26.2 + - - +
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Residues in contact with MET 380 (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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253A LEU* 5.3 0.4 - - - -
341A VAL* 3.7 14.6 - - + -
374A TRP* 3.3 60.5 - - + +
375A LEU* 3.6 35.0 - - + +
377A SER* 3.3 8.4 + - - +
379A ALA* 1.3 77.6 - - - +
381A GLN* 1.3 63.4 + - - +
383A HIS* 3.3 15.8 + - - +
384A VAL* 3.2 23.4 + - - +
403A LEU* 3.8 31.2 - - + -
404A PRO* 3.9 11.7 - - + +
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Residues in contact with GLN 381 (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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339A THR 4.8 1.2 - - - +
340A ARG* 3.2 32.1 + - + +
341A VAL* 2.8 47.4 + - - +
375A LEU 3.0 18.0 + - - -
376A ASN 3.6 10.3 + - - +
377A SER 3.2 19.3 + - - +
378A GLU* 3.9 23.3 - - - +
379A ALA 3.5 0.2 - - - -
380A MET* 1.3 76.2 - - - +
382A LYS* 1.3 61.2 + - - +
384A VAL* 3.4 8.5 - - - +
385A ARG* 3.2 24.7 + - - +
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Residues in contact with LYS 382 (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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249A GLU* 2.7 33.7 + - - -
378A GLU 3.1 18.9 + - - +
379A ALA* 3.9 7.4 - - - +
381A GLN* 1.3 74.8 - - - +
383A HIS* 1.3 57.3 + - - +
385A ARG* 3.9 5.2 - - - +
386A THR* 2.7 44.2 + - - +
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Residues in contact with HIS 383 (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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250A THR* 3.5 39.4 - - - +
253A LEU* 3.5 27.6 - - + +
254A GLU* 3.8 16.8 + - + +
379A ALA 3.1 19.7 + - - +
380A MET* 3.3 10.3 + - - +
382A LYS* 1.3 77.8 - - - +
384A VAL* 1.3 62.4 + - + +
386A THR* 3.5 4.3 + - - -
387A LEU* 3.3 51.1 + - + +
402A ARG 5.3 0.8 + - - -
403A LEU* 4.4 15.8 - - + +
404A PRO* 4.1 16.7 - - + +
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Residues in contact with VAL 384 (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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339A THR* 3.6 15.2 - - + +
340A ARG* 3.8 28.0 - - - -
341A VAL* 3.9 13.9 - - + -
380A MET 3.4 9.4 - - - +
381A GLN* 3.4 17.3 - - - +
383A HIS* 1.3 75.8 - - + +
385A ARG* 1.3 59.0 + - - +
388A TYR* 2.9 49.2 + - + +
395A LEU* 4.0 11.4 - - + -
403A LEU* 3.7 30.5 - - + -
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Residues in contact with ARG 385 (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 TYR* 5.3 1.2 + - - -
339A THR 4.4 13.0 - - - +
381A GLN 3.2 20.0 + - - +
382A LYS* 4.0 5.6 - - - +
383A HIS 3.4 0.2 - - - -
384A VAL* 1.3 75.2 - - - +
386A THR* 1.3 62.3 + - - +
389A ARG* 3.0 73.9 + - - +
390A ASP* 4.0 18.5 + - - +
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Residues in contact with THR 386 (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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232A TRP* 5.1 4.5 - - + -
245A PHE* 3.1 33.2 - - - +
247A THR* 3.9 11.2 - - + +
249A GLU* 3.8 22.9 + - - +
250A THR* 3.8 15.0 - - + -
382A LYS* 2.7 32.3 + - - +
383A HIS* 3.7 5.1 - - - -
384A VAL 3.3 0.2 - - - -
385A ARG* 1.3 79.8 - - - +
387A LEU* 1.3 61.5 + - - +
389A ARG* 4.0 7.2 + - - +
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Residues in contact with LEU 387 (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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244A ARG* 3.5 50.0 - - + +
245A PHE* 3.0 27.9 + - - +
246A GLU* 3.8 14.1 - - + -
250A THR* 3.8 27.8 - - + +
254A GLU* 4.2 1.1 - - - +
383A HIS* 3.3 45.3 + - + +
384A VAL 3.5 0.2 + - - -
386A THR* 1.3 81.1 - - - +
388A TYR* 1.3 86.0 + - + +
389A ARG* 5.0 0.2 - - - -
391A PHE* 3.9 5.4 - - - -
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Residues in contact with TYR 388 (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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170A VAL* 3.8 23.6 - - + -
242A ILE* 4.7 4.0 - - + -
244A ARG* 3.1 45.3 + - + -
339A THR* 3.8 13.2 + - + -
384A VAL* 2.9 35.9 + - + +
387A LEU* 1.3 96.1 - - + +
389A ARG* 1.3 70.4 + - - +
390A ASP 3.1 0.2 + - - -
391A PHE* 3.1 32.4 + - + +
392A VAL 4.9 0.2 + - - -
398A ARG 4.4 3.9 + - - -
399A MET* 3.6 58.1 + - + -
402A ARG* 4.7 5.0 - - - +
403A LEU* 5.8 0.7 - - + -
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Residues in contact with ARG 389 (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 TYR* 3.2 35.1 - - - +
219A ASP* 3.0 42.4 + - - -
232A TRP* 3.6 23.0 - - - -
245A PHE* 3.7 31.7 - - + +
339A THR* 3.2 25.8 + - - -
384A VAL 3.8 1.6 + - - -
385A ARG* 3.0 51.2 + - - +
386A THR* 4.0 8.1 + - - +
388A TYR* 1.3 76.4 - - - +
390A ASP* 1.3 66.2 + - - +
391A PHE* 4.1 9.6 - - + -
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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