Contacts of the helix formed by residues 346 - 357 (chain A) in PDB entry 3D14
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 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ALA* 3.2 3.6 - - - +
345A HIS* 1.3 92.4 - - + +
347A TYR* 1.3 63.7 + - - +
348A GLN* 3.6 14.5 + - - +
349A GLU* 2.9 28.6 + - - +
350A THR* 3.1 24.5 + - - -
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Residues in contact with TYR 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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305A THR* 5.9 2.0 - - - -
306A LEU* 3.7 48.0 - - + +
314A ILE 5.6 0.7 + - - -
346A THR* 1.3 71.3 - - - +
348A GLN* 1.3 81.5 + - + +
350A THR* 3.3 7.0 + - - -
351A TYR* 2.9 46.3 + + + +
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Residues in contact with GLN 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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346A THR* 3.2 11.8 - - - +
347A TYR* 1.3 106.0 + - + +
349A GLU* 1.3 55.7 + - - +
351A TYR* 3.5 6.3 - - - +
352A ARG* 3.0 39.6 + - - +
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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
----------------------------------------------------------
344A ALA* 3.5 14.6 - - + -
346A THR* 2.9 19.2 + - + +
348A GLN* 1.3 73.4 - - - +
350A THR* 1.3 61.5 + - - +
352A ARG* 2.9 37.5 + - - +
353A ARG* 2.7 71.9 + - - +
358A GLU* 5.4 0.2 - - - +
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Residues in contact with THR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 6.1 0.7 - - - -
306A LEU* 3.9 18.4 - - + +
307A ASP* 4.1 15.0 + - - +
342A PHE* 2.9 28.8 + - + +
343A GLU* 4.3 0.2 - - - -
344A ALA* 3.3 18.7 + - - +
346A THR 3.1 14.0 + - - -
347A TYR* 3.7 7.0 - - - -
349A GLU* 1.3 75.0 - - - +
351A TYR* 1.3 58.0 + - - +
353A ARG* 3.3 2.5 + - - +
354A ILE* 2.9 55.1 + - + +
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Residues in contact with TYR 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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306A LEU* 3.8 21.2 - - + +
314A ILE* 3.4 46.9 + - + +
315A GLU* 3.5 23.0 - - + +
347A TYR* 2.9 34.7 + + + +
348A GLN* 3.5 9.2 - - - +
350A THR* 1.3 76.2 - - - +
352A ARG* 1.3 65.9 + - - +
354A ILE 3.5 0.2 + - - -
355A SER* 3.0 30.9 + - - -
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Residues in contact with ARG 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLN* 3.0 21.1 + - - +
349A GLU* 2.9 51.0 + - - +
351A TYR* 1.3 79.0 - - - +
353A ARG* 1.3 66.3 + - + +
355A SER* 3.4 4.4 + - - -
356A ARG* 3.2 66.5 + - - +
358A GLU* 5.3 1.1 - - - -
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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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341A PRO 3.8 10.9 + - - -
342A PHE* 3.6 24.8 - - + -
343A GLU 2.7 28.4 + - - +
344A ALA* 4.2 1.4 - - - +
349A GLU* 2.7 69.3 + - - +
350A THR* 4.1 2.7 - - - +
352A ARG* 1.3 74.8 - - + +
354A ILE* 1.3 60.9 + - - +
356A ARG 3.5 0.5 + - - -
357A VAL* 2.9 8.0 + - - -
358A GLU* 2.8 78.5 + - - +
359A PHE* 5.4 1.0 - - - +
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Residues in contact with ILE 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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306A LEU* 3.3 36.6 - - + +
307A ASP 4.7 3.4 - - - +
309A LEU 3.6 20.0 - - - +
311A PRO* 3.6 24.2 - - + +
314A ILE* 3.5 21.8 - - + -
326A TRP* 4.1 4.5 - - + -
342A PHE* 3.6 30.3 - - + -
350A THR* 2.9 33.5 + - + +
353A ARG* 1.3 73.9 - - - +
355A SER* 1.3 66.3 + - - +
357A VAL* 2.9 20.4 + - - +
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Residues in contact with SER 355 (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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311A PRO* 4.8 2.5 - - - -
314A ILE* 4.2 1.1 - - - +
315A GLU* 3.4 24.7 + - - -
351A TYR* 3.0 30.4 + - - -
352A ARG* 3.7 6.3 - - - -
353A ARG 3.4 0.2 - - - -
354A ILE* 1.3 78.3 - - - +
356A ARG* 1.3 60.6 + - - +
379A HIS* 3.3 25.5 + - - -
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Residues in contact with ARG 356 (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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352A ARG* 3.2 45.4 + - - +
355A SER* 1.3 78.6 - - - +
357A VAL* 1.3 69.8 + - - +
358A GLU* 3.2 39.8 + - + +
379A HIS* 5.6 0.2 - - - -
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Residues in contact with VAL 357 (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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326A TRP* 3.9 20.2 - - + -
342A PHE* 4.1 7.9 - - + -
353A ARG 2.9 7.8 + - - -
354A ILE 2.9 13.3 + - - +
356A ARG* 1.3 80.2 - - - +
358A GLU* 1.3 59.8 + - - +
359A PHE* 3.6 23.9 + - + +
377A LEU* 3.2 24.9 - - + +
379A HIS* 3.8 35.2 - - + +
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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