Contacts of the helix formed by residues 300 - 310 (chain A) in PDB entry 4FO9
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 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PHE* 4.3 0.9 - - - -
197A PHE 5.3 8.3 - - - +
199A PRO* 5.9 6.1 - - + -
298A GLN* 5.6 1.6 - - + +
299A LEU* 1.3 75.0 - - - +
301A SER* 1.3 64.9 + - - +
302A ALA* 3.3 10.0 + - - +
303A MET* 3.1 36.8 + - - +
304A LEU* 3.1 26.9 + - - +
378A GLU* 3.2 11.4 - - - +
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Residues in contact with SER 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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153A PHE* 4.2 8.1 - - - -
300A THR* 1.3 72.5 - - - +
302A ALA* 1.3 59.8 + - - +
304A LEU* 3.2 4.3 + - - +
305A LEU* 2.8 30.5 + - - +
371A ALA 4.9 0.9 - - - -
374A LEU* 4.0 31.9 - - - +
375A GLN* 4.0 15.5 - - - +
378A GLU* 3.1 25.2 + - - -
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Residues in contact with ALA 302 (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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300A THR* 3.2 9.7 + - - +
301A SER* 1.3 79.4 + - - +
303A MET* 1.3 59.5 + - + +
305A LEU* 3.3 9.4 + - - +
306A GLN* 2.8 30.5 + - - +
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Residues in contact with MET 303 (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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297A ARG* 4.6 13.0 - - - -
298A GLN 4.8 2.7 - - - +
299A LEU* 4.0 31.4 - - + -
300A THR* 3.1 39.4 + - - +
301A SER 3.1 0.2 - - - -
302A ALA* 1.3 79.1 - - + +
304A LEU* 1.3 63.2 + - - +
306A GLN* 3.3 8.0 + - - +
307A ARG* 3.0 36.3 + - - +
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Residues in contact with LEU 304 (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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152A PRO* 3.4 24.0 - - + +
153A PHE* 3.6 28.5 - - + -
299A LEU* 3.7 24.2 - - + -
300A THR 3.1 26.3 + - - +
301A SER* 3.7 7.0 - - - +
303A MET* 1.3 76.1 - - - +
305A LEU* 1.3 63.5 + - - +
307A ARG* 3.2 8.5 + - - +
308A LEU* 2.9 22.2 + - - +
374A LEU* 3.9 15.9 - - + -
394A TYR* 3.0 47.3 + - + +
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Residues in contact with LEU 305 (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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301A SER 2.8 14.5 + - - +
302A ALA* 3.3 13.5 - - - +
304A LEU* 1.3 72.4 - - - +
306A GLN* 1.3 66.4 + - - +
308A LEU* 2.9 11.8 + - + +
309A LYS* 2.9 46.5 + - + +
355A ILE* 4.7 14.6 - - + -
370A ALA* 3.9 25.8 - - + -
371A ALA* 3.7 28.5 - - + -
374A LEU* 3.6 12.0 - - + +
399A LEU* 5.7 0.2 - - + -
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Residues in contact with GLN 306 (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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302A ALA 2.8 17.3 + - - +
303A MET* 3.5 10.8 - - - +
305A LEU* 1.3 75.0 - - - +
307A ARG* 1.3 64.5 + - + +
309A LYS* 3.2 21.2 + - - +
310A MET* 3.3 21.9 + - - +
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Residues in contact with ARG 307 (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 ASP* 2.9 41.8 + - - -
299A LEU* 3.5 21.7 - - - +
303A MET* 3.0 26.6 + - - +
304A LEU* 3.7 8.9 - - - +
305A LEU 3.2 0.4 - - - -
306A GLN* 1.3 77.7 - - + +
308A LEU* 1.3 61.3 + - - +
310A MET* 3.2 24.4 + - - +
311A LYS* 3.4 13.2 + - - +
394A TYR* 3.6 15.9 - - - +
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Residues in contact with LEU 308 (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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304A LEU 2.9 12.1 + - - +
305A LEU* 2.9 11.6 + - + +
307A ARG* 1.3 77.1 - - - +
309A LYS* 1.3 62.6 + - - +
311A LYS* 3.1 24.3 + - + +
313A ILE 5.4 0.2 + - - -
357A CYS* 4.6 0.7 - - - -
370A ALA* 4.4 11.7 - - + -
374A LEU* 4.4 17.5 - - + -
394A TYR* 3.5 15.7 + - + +
397A LEU* 3.7 51.8 - - + +
398A ILE* 5.0 0.4 - - - -
399A LEU* 4.0 33.5 - - + +
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Residues in contact with LYS 309 (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 LEU* 2.9 41.7 + - + +
306A GLN* 3.5 13.2 - - - +
308A LEU* 1.3 76.5 - - - +
310A MET* 1.3 60.1 + - + +
311A LYS 3.3 2.4 + - - +
313A ILE* 4.1 18.5 - - + +
355A ILE* 4.5 21.1 - - + -
399A LEU* 4.1 17.9 - - + +
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Residues in contact with MET 310 (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 GLN* 3.4 19.3 - - + +
307A ARG* 3.2 18.8 + - - +
309A LYS* 1.3 77.0 - - + +
311A LYS* 1.3 60.0 + - - +
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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