Contacts of the helix formed by residues 337 - 344 (chain E) in PDB entry 3A2C
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 337 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257E LEU 4.7 3.6 + - - -
258E CYS 3.9 2.5 - - - +
289E PRO* 3.8 27.9 - - + +
290E GLU* 3.7 43.3 + - + +
293E GLU* 6.3 2.9 - - + -
335E PRO 4.8 4.9 + - - -
336E LEU* 1.3 74.5 - - - +
338E THR* 1.3 57.4 + - - +
339E SER 3.4 1.7 + - - -
340E ARG* 2.9 37.4 + - + +
341E VAL* 2.8 44.1 + - + +
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Residues in contact with THR 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E PHE* 5.2 0.4 - - + -
150E ILE* 4.2 14.1 - - + -
158E PHE* 3.8 14.4 - - + -
255E ILE 4.0 2.7 - - - +
256E LEU* 2.5 32.5 + - - +
257E LEU 3.3 15.2 + - - -
258E CYS 3.7 8.9 + - - -
259E GLY* 3.9 5.4 - - - -
336E LEU* 3.1 8.8 - - - +
337E HIS* 1.3 77.9 - - - +
339E SER* 1.3 54.3 + - - +
341E VAL* 3.7 0.7 - - - +
342E LEU* 2.7 63.7 + - + +
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Residues in contact with SER 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ILE* 3.3 32.3 + - - +
151E GLN* 4.2 1.3 - - - +
153E ARG* 4.6 11.4 - - - -
154E GLY* 3.6 10.6 + - - -
156E GLN 5.4 1.8 - - - -
158E PHE* 4.8 6.4 - - - +
336E LEU 4.8 2.2 + - - -
337E HIS 3.5 0.4 - - - -
338E THR* 1.3 74.5 - - - +
340E ARG* 1.3 69.3 + - - +
342E LEU* 3.2 5.6 + - - +
343E LYS* 2.9 48.0 + - - +
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Residues in contact with ARG 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ASP* 6.2 6.1 - - + -
335E PRO* 5.3 7.5 - - - +
336E LEU 3.6 15.4 + - - +
337E HIS* 2.9 62.0 + - + +
339E SER* 1.3 79.6 + - - +
341E VAL* 1.3 62.8 + - + +
343E LYS* 3.4 11.8 - - + +
344E GLU* 3.1 33.2 + - - +
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Residues in contact with VAL 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E CYS 3.5 15.0 - - - +
259E GLY 3.4 25.8 - - - +
260E TYR* 4.1 12.1 - - + -
290E GLU* 4.1 11.7 - - - +
337E HIS* 2.8 38.2 + - + +
338E THR 3.7 0.9 - - - +
340E ARG* 1.3 69.7 - - + +
342E LEU* 1.3 67.2 + - - +
343E LYS 3.0 1.6 - - - -
344E GLU* 2.8 32.9 + - - +
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Residues in contact with LEU 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E PDY 4.1 29.6 - - + +
147E PHE* 4.4 29.8 - - + +
150E ILE* 4.7 3.4 - - + -
151E GLN* 3.2 34.9 + - + +
255E ILE* 4.9 0.7 - - + -
259E GLY* 3.5 24.7 - - - +
338E THR* 2.7 56.7 + - + +
339E SER* 3.8 2.7 - - - +
341E VAL* 1.3 72.0 - - - +
343E LYS* 1.3 62.2 + - - +
344E GLU 3.1 9.0 - - - +
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Residues in contact with LYS 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E GLN* 3.5 34.2 + - + +
152E ASP* 4.8 1.4 - - - +
153E ARG 4.3 2.8 - - - +
154E GLY* 3.7 25.2 + - - +
339E SER* 2.9 36.6 + - - +
340E ARG* 3.4 13.5 - - + +
342E LEU* 1.3 78.4 - - - +
344E GLU* 1.3 65.1 + - + +
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Residues in contact with GLU 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340E ARG* 3.1 23.8 - - - +
341E VAL* 2.8 24.1 + - + +
342E LEU 3.1 10.2 - - - +
343E LYS* 1.3 79.3 - - + +
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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