Contacts of the helix formed by residues 344 - 354 (chain A) in PDB entry 3DCT
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 HIS 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A THR* 3.1 30.4 + - - -
271A ASN* 4.5 8.3 + - - -
273A ILE* 3.8 16.2 - - + +
274A LEU* 3.9 36.0 - - + +
340A LEU 3.5 3.0 + - - -
341A PRO 3.3 22.3 + - - -
342A SER* 3.7 14.8 + - - -
343A GLY* 1.3 77.9 - - - +
345A SER* 1.3 55.2 + - - +
346A ASP 3.3 2.5 - - - -
347A LEU* 2.8 18.1 + - + -
348A LEU 2.7 29.8 + - - -
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Residues in contact with SER 345 (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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335A ILE* 3.7 19.5 + - - +
336A PHE* 3.5 29.7 - - - -
339A LYS* 3.8 19.7 - - - +
340A LEU 4.2 2.3 + - - -
343A GLY 3.0 5.2 + - - -
344A HIS* 1.3 71.4 - - - +
346A ASP* 1.3 59.2 + - - +
348A LEU* 3.1 1.8 + - - +
349A GLU* 2.7 38.6 + - - +
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Residues in contact with ASP 346 (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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344A HIS 3.1 1.6 + - - -
345A SER* 1.3 80.9 - - - +
347A LEU* 1.3 62.7 + - + +
349A GLU* 3.5 12.0 + - - +
350A GLU* 3.1 29.8 + - - +
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Residues in contact with LEU 347 (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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273A ILE* 3.6 17.5 - - + +
274A LEU* 3.6 39.0 - - + -
278A PHE* 3.6 22.4 - - + -
344A HIS* 2.8 19.1 + - + +
346A ASP* 1.3 76.7 - - + +
348A LEU* 1.3 65.6 + - - +
350A GLU* 3.1 13.1 - - + +
351A ARG* 3.0 26.7 + - - +
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Residues in contact with LEU 348 (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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1A 064 4.9 9.2 - - + -
273A ILE* 3.5 30.0 - - + +
287A LEU* 4.2 23.6 - - + -
290A MET* 4.2 13.9 - - + -
332A SER* 5.9 2.2 - - - -
335A ILE* 4.2 16.2 - - + -
336A PHE* 3.9 22.7 - - + -
343A GLY 3.4 26.0 - - - +
344A HIS 2.7 9.1 + - - -
345A SER 3.4 7.0 - - - +
347A LEU* 1.3 75.4 - - - +
349A GLU* 1.3 62.2 + - - +
351A ARG* 3.2 6.9 + - + +
352A ILE* 3.0 28.6 + - + +
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Residues in contact with GLU 349 (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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336A PHE* 3.9 16.7 - - + -
345A SER 2.7 21.1 + - - +
346A ASP* 3.6 12.4 - - - +
348A LEU* 1.3 72.7 - - - +
350A GLU* 1.3 53.1 + - - +
352A ILE* 3.7 1.2 - - - +
353A ARG* 2.7 72.6 + - + +
366A PHE* 3.2 34.3 - - + -
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Residues in contact with GLU 350 (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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278A PHE* 4.3 15.0 - - + -
283A ASN* 4.4 1.7 + - - -
346A ASP 3.1 20.5 + - - +
347A LEU* 3.1 23.1 - - + +
349A GLU* 1.3 77.6 - - - +
351A ARG* 1.3 62.4 + - - +
353A ARG* 3.1 20.8 + - - +
354A ASN* 3.1 16.5 + - - +
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Residues in contact with ARG 351 (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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272A LYS 3.4 9.3 + - - -
273A ILE* 2.9 35.9 + - - +
276A GLU 2.8 33.9 + - - -
277A GLU 3.0 16.2 + - - -
278A PHE* 3.3 25.7 - - + +
282A GLU* 4.4 0.2 - - - +
283A ASN* 2.4 57.7 + - + +
286A ILE* 3.8 29.7 - - - +
287A LEU* 3.7 9.9 - - + +
347A LEU 3.3 10.5 - - - +
348A LEU* 3.5 9.2 - - + +
350A GLU* 1.3 76.4 - - - +
352A ILE* 1.3 59.5 + - - +
354A ASN 3.2 17.8 - - - +
355A SER* 3.3 11.4 - - - -
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Residues in contact with ILE 352 (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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1A 064 3.8 31.0 - - + -
287A LEU* 3.7 28.9 - - + -
332A SER* 5.8 1.6 - - - -
336A PHE* 4.0 27.6 - - + -
348A LEU* 3.0 25.3 + - + +
349A GLU 3.8 3.4 - - - +
351A ARG* 1.3 72.1 - - - +
353A ARG* 1.3 63.0 + - - +
354A ASN 3.1 4.7 - - - -
355A SER* 3.1 13.7 + - - -
357A ILE* 3.7 5.6 - - + +
362A ILE* 3.5 25.3 - - + +
365A MET* 3.9 10.8 - - - -
366A PHE* 4.0 9.0 - - + -
369A TYR* 5.0 6.1 - - - +
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Residues in contact with ARG 353 (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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349A GLU* 2.7 61.0 + - + +
350A GLU* 3.1 13.4 + - - +
352A ILE* 1.3 75.3 - - - +
354A ASN* 1.3 59.6 + - + +
355A SER 4.0 0.4 - - - -
357A ILE* 5.4 3.3 - - - +
362A ILE* 3.4 36.4 - - - +
363A THR* 5.8 1.0 - - - +
366A PHE* 3.7 29.5 - - + +
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Residues in contact with ASN 354 (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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278A PHE 5.1 2.4 - - - +
279A SER* 4.5 1.4 - - - -
280A ALA* 3.7 28.7 + - - +
283A ASN* 2.8 34.1 + - - +
350A GLU* 3.1 9.4 + - - +
351A ARG 3.4 0.7 - - - -
352A ILE 3.1 0.4 - - - -
353A ARG* 1.3 81.1 + - + +
355A SER* 1.3 59.4 + - - +
356A GLY 4.6 2.4 - - - +
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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