Contacts of the helix formed by residues 293 - 300 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ARG* 2.9 40.9 + - + +
342A ALA 4.1 8.3 - - - +
345A SER* 4.3 2.0 + - - -
291B VAL* 2.9 22.7 + - + +
292B ALA* 1.3 71.1 - - - +
294B GLY* 1.3 64.6 + - - +
296B LEU* 3.8 6.5 - - - +
297B GLY 3.0 11.3 + - - -
305B VAL* 3.8 24.1 - - + +
309B GLN* 3.5 20.9 + - - +
325B CYS* 3.8 24.6 - - - -
326B ALA 2.8 24.2 + - - +
327B THR* 2.8 24.3 + - - -
329B MET* 3.7 11.1 - - - +
346B ASP* 2.7 43.4 + - - -
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ARG* 2.6 34.9 + - - -
177B ASP* 4.5 7.2 - - - -
293B ARG* 1.3 78.5 - - - +
295B ASP* 1.3 60.0 - - - +
297B GLY 3.2 0.3 + - - -
298B ILE* 3.6 6.6 - - - +
327B THR* 3.5 16.2 + - - -
328B GLN* 5.6 0.7 - - - -
534B PYR 3.0 17.5 + - - -
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 5.7 0.5 - - - +
209B ASN* 3.2 25.1 + - - +
243B PHE* 3.5 21.2 - - + -
271B GLU* 2.9 25.3 - - + +
294B GLY* 1.3 72.4 - - - +
296B LEU* 1.3 63.6 + - - +
298B ILE* 3.1 13.1 + - - +
299B GLU* 3.1 24.4 + - - +
533B MG 2.1 30.7 - - - -
534B PYR 3.1 6.4 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ILE 3.7 22.2 - - - +
271B GLU 3.1 14.9 + - - +
272B ASN 4.2 14.6 - - - +
276B VAL* 4.4 7.4 - - + -
291B VAL* 4.4 11.7 - - + -
292B ALA 3.1 17.8 + - - +
293B ARG* 3.8 4.5 - - - +
295B ASP* 1.3 76.5 - - - +
297B GLY* 1.3 57.8 - - - +
298B ILE 3.1 0.3 + - - -
299B GLU 3.3 0.2 + - - -
300B ILE* 2.9 63.3 + - + +
305B VAL* 4.5 12.6 - - + -
308B ALA* 4.1 11.4 - - + -
312B MET* 4.1 23.1 - - + -
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ARG* 2.9 17.0 + - - -
341A ARG* 3.5 26.9 - - - -
293B ARG 3.0 10.9 + - - -
294B GLY 3.2 0.8 + - - -
296B LEU* 1.3 75.1 - - - +
298B ILE* 1.3 55.5 + - - +
300B ILE 2.9 15.8 - - - +
301B PRO* 4.7 0.2 - - - +
302B ALA* 3.8 10.3 + - - -
305B VAL* 3.7 15.0 - - - +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ARG* 4.0 10.5 + - - +
341A ARG* 3.5 13.9 - - - +
174B TYR* 3.7 30.7 - - + -
177B ASP* 3.3 41.5 - - - +
178B GLY* 3.8 6.7 - - - +
209B ASN* 3.7 37.2 - - + +
211B PRO* 3.5 12.5 - - - +
294B GLY 3.6 8.3 - - - +
295B ASP* 3.1 13.6 + - - +
297B GLY* 1.3 80.6 - - - +
299B GLU* 1.3 65.3 + - - +
300B ILE 3.4 2.5 - - - +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ASN* 3.4 32.9 + - - +
210B LEU 3.6 21.0 + - - +
211B PRO* 3.5 28.1 - - - +
215B VAL* 6.1 0.7 - - - +
243B PHE* 5.0 7.4 - - + -
271B GLU 3.5 25.6 - - - +
272B ASN* 3.6 27.6 - - + +
273B HIS* 4.4 5.9 + - + +
295B ASP 3.1 11.5 + - - +
296B LEU 3.9 0.9 - - - +
298B ILE* 1.3 77.8 - - - +
300B ILE* 1.3 60.6 + - + +
301B PRO* 4.9 0.3 - - - +
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.2 18.8 - - + -
273B HIS* 3.6 48.5 - - + +
276B VAL* 5.8 0.2 - - + -
296B LEU* 2.9 39.6 + - + +
297B GLY 2.9 22.7 - - - +
298B ILE 3.9 2.2 - - - -
299B GLU* 1.3 79.2 - - - +
301B PRO* 1.4 86.3 - - + +
304B LYS* 4.0 27.1 - - + +
305B VAL* 4.4 6.3 - - + +
308B ALA* 4.7 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
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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