Contacts of the helix formed by residues 316 - 324 (chain A) in PDB entry 3SHE
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 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LEU 4.8 2.2 + - - -
237A CYS* 4.3 3.4 - - - +
268A PRO* 3.6 24.2 + - + -
269A GLU* 3.7 36.8 - - + +
272A GLU* 5.1 7.7 + - - -
314A PRO 5.1 3.1 + - - -
315A LEU* 1.3 80.1 - - - +
317A THR* 1.3 59.1 + - - +
318A ALA 3.4 2.2 - - - -
319A ARG* 3.0 42.0 + - - +
320A VAL* 2.9 42.5 + - + +
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Residues in contact with THR 317 (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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127A PHE* 5.0 2.0 - - + -
130A ILE* 4.3 6.7 - - + -
138A PHE* 3.9 12.2 - - + -
234A ILE 3.2 18.6 - - - +
235A LEU* 2.5 33.6 + - - +
236A LEU 3.5 3.6 + - - -
237A CYS 3.5 18.0 + - - -
238A GLY* 3.7 4.0 - - - +
315A LEU* 3.4 10.7 - - - +
316A HIS* 1.3 74.5 - - - +
318A ALA* 1.3 57.8 + - - +
320A VAL* 3.3 1.2 + - - +
321A LEU* 2.9 53.5 + - + +
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Residues in contact with ALA 318 (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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130A ILE* 3.4 32.6 - - + +
131A GLN* 4.2 7.0 - - - +
132A GLU 5.1 2.9 - - - +
138A PHE* 4.9 13.7 - - + +
315A LEU 5.1 1.7 + - - +
316A HIS 3.3 0.6 + - - -
317A THR* 1.3 78.0 - - - +
319A ARG* 1.3 62.4 + - - +
321A LEU* 3.5 4.1 + - - +
322A GLN* 3.2 23.6 + - - +
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Residues in contact with ARG 319 (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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268A PRO* 5.8 3.8 - - - +
269A GLU* 3.8 16.2 + - - +
316A HIS* 3.0 45.4 + - - +
318A ALA* 1.3 78.1 - - - +
320A VAL* 1.3 78.7 + - - +
322A GLN* 3.4 4.4 + - - +
323A GLU* 2.9 53.9 + - + +
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Residues in contact with VAL 320 (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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237A CYS 3.2 25.6 - - - +
238A GLY 3.6 18.4 - - - +
239A PHE* 4.0 9.4 - - + -
269A GLU* 4.4 7.9 - - + +
316A HIS* 2.9 24.5 + - + +
317A THR 3.7 2.0 - - - +
319A ARG* 1.3 101.4 - - - +
321A LEU* 1.3 58.2 + - - +
323A GLU* 3.6 8.9 - - - +
324A ASP* 2.9 53.5 + - - +
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Residues in contact with LEU 321 (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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127A PHE* 3.9 26.7 - - + +
130A ILE* 3.8 20.2 - - + -
131A GLN* 3.6 23.0 + - + +
238A GLY* 3.8 20.2 - - - +
317A THR* 2.9 39.5 + - + +
318A ALA* 3.8 0.7 - - - +
319A ARG 3.3 0.2 - - - -
320A VAL* 1.3 73.5 - - - +
322A GLN* 1.3 61.2 + - - +
324A ASP* 3.3 3.0 + - - -
325A LYS* 2.9 31.5 + - - +
328A TRP* 3.9 34.3 - - + +
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Residues in contact with GLN 322 (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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131A GLN* 3.1 45.2 + - - +
318A ALA 3.2 14.6 + - - +
319A ARG* 3.8 4.0 - - - +
321A LEU* 1.3 77.4 - - - +
323A GLU* 1.3 63.1 + - - +
325A LYS* 3.4 16.6 + - - +
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Residues in contact with GLU 323 (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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319A ARG* 2.9 50.6 + - + +
320A VAL* 3.6 8.0 - - - +
322A GLN* 1.3 78.3 - - - +
324A ASP* 1.3 67.9 + - - +
325A LYS 3.5 0.7 + - - -
326A ASP* 5.2 1.6 + - - +
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Residues in contact with ASP 324 (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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238A GLY 5.0 3.8 - - - +
239A PHE* 5.2 5.9 - - - +
320A VAL* 2.9 38.1 + - + +
321A LEU* 3.4 4.3 - - - +
323A GLU* 1.3 89.2 - - - +
325A LYS* 1.3 63.5 + - - +
326A ASP* 3.0 5.4 + - - -
327A HIS* 3.1 33.3 + - - +
328A TRP* 3.7 7.7 + - - +
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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