Contacts of the helix formed by residues 294 - 301 (chain A) in PDB entry 3R1N
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 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A MET* 3.9 4.3 - - - -
292A ARG 3.5 2.6 + - - -
293A LEU* 1.3 75.0 - - - +
295A ILE* 1.3 68.6 + - + +
296A THR* 3.3 27.8 + - + +
297A GLN* 3.0 26.9 + - + -
298A PHE* 2.9 26.5 + - - +
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Residues in contact with ILE 295 (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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151A GLY 3.4 18.8 - - - +
154A ILE* 3.6 16.8 - - + -
155A GLN* 3.7 31.6 - - + +
158A HIS* 4.0 29.9 + - + +
159A SER 5.9 0.2 - - - +
225A MET* 3.7 18.5 - - + +
228A LEU* 3.8 21.1 - - + -
294A THR* 1.3 80.1 - - + +
296A THR* 1.3 71.3 + - + +
298A PHE* 3.3 11.3 + - + +
299A MET* 3.0 27.2 + - + +
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Residues in contact with THR 296 (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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155A GLN* 5.0 10.1 - - + +
294A THR* 3.2 17.9 - - + -
295A ILE* 1.3 84.8 - - + +
297A GLN* 1.3 63.2 + - - +
299A MET* 3.6 4.9 + - - -
300A ASN* 3.2 38.3 + - - +
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Residues in contact with GLN 297 (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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292A ARG 4.5 1.4 - - - +
293A LEU* 3.5 30.9 - - + +
294A THR* 3.0 38.6 + - + +
295A ILE 3.3 0.2 - - - -
296A THR* 1.3 78.9 - - - +
298A PHE* 1.3 63.6 + - - +
300A ASN* 3.8 5.1 - - - +
301A HIS* 3.1 21.7 + - - +
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Residues in contact with PHE 298 (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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147A MET* 3.7 26.5 - - + -
151A GLY* 3.7 22.2 - - - -
225A MET* 3.6 14.4 - - + -
228A LEU* 4.2 8.5 - - + -
232A MET* 5.1 1.1 - - - -
280A LEU* 4.1 11.0 - - + -
284A LEU* 4.0 34.1 - - + -
293A LEU* 4.2 10.5 - - + +
294A THR 2.9 14.8 + - - +
295A ILE* 3.3 20.8 + - + +
297A GLN* 1.3 76.0 - - - +
299A MET* 1.3 68.0 + - - +
301A HIS* 3.1 23.8 + - - +
304A ILE* 3.2 47.4 - - + +
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Residues in contact with MET 299 (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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148A ARG* 4.2 14.4 - - + +
151A GLY* 3.6 33.0 - - - +
152A THR* 3.7 23.8 - - + -
155A GLN* 3.7 32.8 - - - +
295A ILE* 3.0 21.2 + - + +
296A THR 4.1 3.8 - - - +
298A PHE* 1.3 82.0 - - + +
300A ASN* 1.3 64.4 + - - +
301A HIS 3.5 0.2 - - - -
304A ILE* 3.8 19.1 - - + +
305A ASN* 3.3 27.4 + - - +
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Residues in contact with ASN 300 (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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155A GLN* 6.1 0.4 - - - +
296A THR* 3.2 27.0 + - - +
297A GLN* 3.8 5.6 - - - +
298A PHE 3.2 0.8 - - - -
299A MET* 1.3 81.3 + - - +
301A HIS* 1.3 65.5 + - - +
302A PRO* 3.5 4.2 - - - +
305A ASN* 4.0 17.9 - - - +
306A GLN* 5.3 1.4 + - - -
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Residues in contact with HIS 301 (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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276A ASP* 3.6 28.9 - - + -
279A GLN* 3.3 30.2 + - - +
280A LEU* 3.7 31.5 - - + +
283A LEU* 4.6 11.2 - - + -
293A LEU* 4.9 1.8 - - + -
297A GLN 3.1 12.5 + - - +
298A PHE 3.1 14.7 + - - +
300A ASN* 1.3 77.4 - - - +
302A PRO* 1.4 72.0 - - + +
303A TRP* 3.1 32.2 + - + +
304A ILE* 2.9 4.8 + - - +
305A ASN* 2.7 32.3 + - - -
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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