Contacts of the helix formed by residues 293 - 300 (chain H) in PDB entry 3SRF
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 ARG 293 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341G ARG* 2.9 54.7 + - + +
342G ALA 3.9 0.8 - - - +
345G SER* 4.4 2.8 + - - -
291H VAL* 3.0 30.7 + - + -
292H ALA* 1.3 71.0 - - - +
294H GLY* 1.3 56.7 + - - +
296H LEU* 3.7 4.7 - - - +
297H GLY 2.9 19.8 + - - -
305H VAL* 3.8 22.8 - - + +
309H GLN* 3.6 24.5 + - + +
325H CYS* 3.8 21.1 - - - -
326H ALA 2.7 25.2 + - - +
327H THR* 3.1 20.0 + - - -
328H GLN 4.2 1.2 + - - -
329H MET* 3.7 5.9 - - - -
346H ASP* 2.9 39.3 + - - -
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Residues in contact with GLY 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341G ARG* 2.9 30.5 + - - +
177H ASP* 4.9 4.0 - - - -
292H ALA 3.3 1.6 + - - -
293H ARG* 1.3 77.7 - - - +
295H ASP* 1.3 62.8 + - - +
297H GLY 3.4 1.2 + - - -
298H ILE* 3.4 10.3 - - - +
327H THR* 3.6 19.5 + - - -
328H GLN* 3.9 6.3 - - - -
534H PYR 3.3 13.7 + - - -
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Residues in contact with ASP 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H ASN* 3.6 17.1 + - - +
243H PHE* 4.1 16.5 - - + -
271H GLU* 2.6 27.6 - - + +
294H GLY* 1.3 74.3 - - - +
296H LEU* 1.3 61.5 + - - +
298H ILE* 3.2 20.5 + - - +
299H GLU* 3.3 17.5 + - - +
533H MG 2.2 32.1 - - - -
534H PYR 3.1 13.6 + - - +
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Residues in contact with LEU 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270H ILE 3.5 23.6 - - - +
271H GLU 3.4 12.7 + - - +
272H ASN* 4.1 10.5 - - - +
276H VAL* 4.3 15.3 - - + -
291H VAL* 4.7 6.7 - - + -
292H ALA 3.2 18.3 + - - +
293H ARG* 3.7 5.6 - - - +
295H ASP* 1.3 74.1 - - - +
297H GLY* 1.3 56.9 + - - +
298H ILE 3.0 5.2 - - - -
299H GLU 4.5 0.2 - - - +
300H ILE* 3.0 71.3 + - + +
305H VAL* 4.7 7.9 - - + -
308H ALA* 4.5 5.6 - - + -
312H MET* 4.1 24.2 - - + -
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Residues in contact with GLY 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G ARG* 3.2 23.0 + - - -
341G ARG* 3.7 19.4 + - - -
293H ARG 2.9 10.9 + - - -
294H GLY 3.4 0.2 + - - -
295H ASP 3.3 0.6 - - - -
296H LEU* 1.3 74.2 - - - +
298H ILE* 1.3 60.2 + - - +
300H ILE 3.5 10.6 - - - +
302H ALA* 4.0 6.9 - - - +
305H VAL* 3.7 23.7 - - - +
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Residues in contact with ILE 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338G ARG* 4.8 7.2 - - - +
341G ARG* 3.8 6.1 - - - +
174H TYR* 3.7 30.7 - - + -
177H ASP* 3.5 36.1 - - - +
178H GLY* 4.2 4.7 - - - -
209H ASN* 3.5 44.4 - - + +
211H PRO* 3.6 12.9 - - - +
294H GLY 3.4 19.7 - - - +
295H ASP* 3.6 9.4 - - - +
296H LEU 3.0 0.6 - - - -
297H GLY* 1.3 83.0 - - - +
299H GLU* 1.3 63.2 + - - +
300H ILE 3.5 3.2 - - - +
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Residues in contact with GLU 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209H ASN* 3.3 29.7 + - - +
210H LEU 3.7 12.6 + - - +
211H PRO* 3.5 38.2 - - - +
212H GLY 4.8 0.9 + - - -
243H PHE* 5.7 4.8 - - + -
271H GLU 3.2 27.1 - - - +
272H ASN* 3.9 24.7 - - + +
273H HIS* 4.4 7.3 - - + +
295H ASP* 3.4 7.2 - - + +
296H LEU 3.2 3.0 + - - +
298H ILE* 1.3 78.3 - - - +
300H ILE* 1.3 60.7 + - - +
301H PRO* 4.7 1.2 - - - +
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Residues in contact with ILE 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 4.1 19.1 - - + -
338G ARG* 5.3 0.2 + - - -
273H HIS* 3.9 37.9 - - + +
296H LEU* 3.0 42.3 + - + +
297H GLY 3.5 16.3 - - - +
298H ILE 3.9 2.5 - - - +
299H GLU* 1.3 80.6 - - - +
301H PRO* 1.3 78.1 - - + +
302H ALA 3.4 1.9 + - - -
304H LYS* 3.8 37.5 - - + +
305H VAL* 4.1 8.1 - - + +
308H ALA* 4.8 3.1 - - + -
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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
------------------------------------------------------------
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