Contacts of the helix formed by residues 221 - 235 (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 SER 221 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114H LYS* 6.1 0.5 - - - +
115H GLY 4.8 5.6 + - - -
116H PRO* 6.1 1.1 - - - -
218H PRO* 4.0 23.8 + - - -
219H ALA 4.0 1.4 - - - -
220H VAL* 1.3 75.6 - - - +
222H GLU* 1.3 67.6 + - - +
223H LYS* 3.7 9.6 + - - +
224H ASP* 2.8 35.6 + - - -
225H ILE* 2.9 30.8 + - - +
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Residues in contact with GLU 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PRO* 4.9 6.8 - - - +
221H SER* 1.3 82.3 - - - +
223H LYS* 1.3 63.6 + - + +
225H ILE* 3.5 13.7 + - + +
226H GLN* 3.3 27.7 + - - +
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Residues in contact with LYS 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H PHE 3.9 17.1 + - - -
76H SER 5.3 3.9 + - - -
77H HIS 6.2 1.0 - - - -
78H GLY 5.0 8.3 + - - -
114H LYS* 3.7 39.7 - - + +
221H SER* 3.2 8.7 - - - +
222H GLU* 1.3 81.6 - - + +
224H ASP* 1.3 59.3 + - - +
226H GLN* 3.3 8.7 + - + +
227H ASP* 3.0 46.0 + - - +
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Residues in contact with ASP 224 (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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113H THR* 4.0 13.8 - - + +
114H LYS* 3.5 16.9 + - - +
115H GLY* 3.1 40.5 + - - -
219H ALA 3.9 5.2 - - - +
220H VAL* 4.1 9.6 - - + -
221H SER* 2.8 37.0 + - - +
223H LYS* 1.3 76.6 - - - +
225H ILE* 1.3 53.6 + - - +
227H ASP* 3.1 9.4 + - - +
228H LEU* 2.7 41.5 + - + +
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Residues in contact with ILE 225 (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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220H VAL* 3.7 20.2 - - + +
221H SER 2.9 19.8 + - - +
222H GLU* 3.8 14.4 - - - +
223H LYS 3.3 0.4 - - - -
224H ASP* 1.3 75.2 - - - +
226H GLN* 1.3 61.7 + - - +
228H LEU* 3.8 1.3 - - - +
229H LYS* 2.9 55.6 + - + +
252H GLU* 5.5 4.3 - - - +
256H VAL* 4.0 26.9 - - + -
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Residues in contact with GLN 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H HIS* 3.2 23.3 - - + +
222H GLU 3.3 13.9 + - - +
223H LYS* 3.3 11.6 + - + +
224H ASP 3.2 0.4 - - - -
225H ILE* 1.3 82.1 - - - +
227H ASP* 1.3 60.7 + - - +
229H LYS* 4.1 11.8 - - - +
230H PHE* 3.1 21.5 + - - +
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Residues in contact with ASP 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H PHE* 3.4 38.3 - - + +
80H HIS* 2.8 27.5 + - - -
111H LEU* 3.5 18.1 - - + +
113H THR* 5.0 3.4 - - + -
114H LYS 4.7 0.7 + - - -
223H LYS* 3.0 43.0 + - - +
224H ASP* 3.5 16.0 - - - +
226H GLN* 1.3 75.8 - - - +
228H LEU* 1.3 57.7 + - - +
230H PHE* 3.3 4.8 - - - +
231H GLY 3.1 20.4 + - - -
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Residues in contact with LEU 228 (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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111H LEU* 4.8 3.6 - - + -
113H THR* 4.1 17.3 - - + -
220H VAL* 4.2 17.9 - - + -
224H ASP* 2.7 23.9 + - + +
225H ILE 3.8 0.2 - - - +
227H ASP* 1.3 71.2 - - - +
229H LYS* 1.3 65.0 + - - +
231H GLY* 3.1 11.8 + - - -
232H VAL* 3.2 17.6 + - - +
239H VAL* 3.9 39.5 - - + -
253H VAL* 3.9 24.5 - - + +
256H VAL* 3.7 31.6 - - + -
257H LEU* 4.1 13.9 - - + +
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Residues in contact with LYS 229 (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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225H ILE* 2.9 43.9 + - + +
226H GLN* 4.1 13.0 - - - +
228H LEU* 1.3 71.0 - - - +
230H PHE* 1.3 60.3 + - - +
232H VAL* 3.4 19.2 + - + +
233H GLU* 3.5 18.9 + - - +
256H VAL* 4.1 22.7 + - + +
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Residues in contact with PHE 230 (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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75H PHE* 3.9 31.0 - + - -
80H HIS* 3.0 56.3 - + + -
83H HIS* 4.3 7.4 - - + -
84H ALA* 3.9 7.4 - - + -
87H ILE* 4.7 5.8 - - + -
111H LEU* 5.0 0.2 - - + -
226H GLN 3.1 20.6 + - - +
227H ASP 3.3 5.8 - - - +
229H LYS* 1.3 77.0 - - - +
231H GLY* 1.3 64.1 + - - +
233H GLU* 3.3 19.1 - - - +
234H GLN* 3.1 65.5 + - + +
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Residues in contact with GLY 231 (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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111H LEU* 3.6 23.3 - - - -
227H ASP 3.1 7.3 + - - -
228H LEU 3.1 8.4 + - - -
230H PHE* 1.3 78.5 - - - +
232H VAL* 1.3 61.3 + - - +
234H GLN* 3.5 1.5 + - - -
235H ASP 3.0 17.7 + - - -
236H VAL* 3.0 30.4 + - - +
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Residues in contact with VAL 232 (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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228H LEU 3.2 15.0 + - - +
229H LYS* 3.7 11.2 - - - +
230H PHE 3.3 0.4 - - - -
231H GLY* 1.3 76.1 - - - +
233H GLU* 1.3 57.6 + - - +
235H ASP* 3.2 19.4 + - - +
256H VAL 5.1 1.3 - - - +
257H LEU* 3.9 36.1 - - + +
260H LYS* 3.6 46.2 - - + +
261H GLY* 4.0 1.6 - - - +
264H ILE* 4.3 10.5 - - + +
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Residues in contact with GLU 233 (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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229H LYS* 3.5 13.6 + - - +
230H PHE* 3.3 29.3 - - + +
232H VAL* 1.3 75.7 - - - +
234H GLN* 1.3 65.6 + - + +
235H ASP* 3.1 8.3 + - - +
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Residues in contact with GLN 234 (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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84H ALA* 3.8 20.8 - - - +
87H ILE* 3.9 33.2 - - + +
91H ARG* 2.8 41.3 + - - +
230H PHE* 3.1 61.9 + - + +
231H GLY* 4.0 5.4 - - - +
232H VAL 3.4 0.2 - - - -
233H GLU* 1.3 79.6 - - + +
235H ASP* 1.3 56.0 - - - +
236H VAL* 4.7 0.9 - - + -
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Residues in contact with ASP 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ARG* 2.8 22.5 + - - +
231H GLY 3.0 3.6 + - - -
232H VAL 3.2 11.2 + - - +
233H GLU 3.1 6.3 - - - +
234H GLN* 1.3 79.6 - - - +
236H VAL* 1.3 63.5 + - - +
237H ASP* 4.0 5.9 + - - +
264H ILE* 6.2 0.2 - - - -
457H GLN* 4.3 15.9 + - - -
460H ARG* 3.8 20.6 + - - -
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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