Contacts of the helix formed by residues 221 - 234 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114G LYS* 5.4 6.6 + - - +
115G GLY 5.5 3.4 + - - -
116G PRO* 6.3 0.7 - - - -
218G PRO* 4.1 17.2 + - - -
219G ALA 4.0 0.4 - - - -
220G VAL* 1.3 77.3 - - - +
222G GLU* 1.3 71.4 + - - +
223G LYS* 3.3 10.8 + - - +
224G ASP* 2.8 33.5 + - - -
225G ILE* 3.0 30.1 + - - +
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Residues in contact with GLU 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G PRO* 5.5 2.3 - - - +
221G SER* 1.3 84.5 - - - +
223G LYS* 1.3 64.2 + - + +
225G ILE* 3.4 17.0 + - + +
226G GLN* 3.2 27.4 + - - +
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Residues in contact with LYS 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G PHE* 3.9 18.0 + - - -
76G SER* 5.8 0.7 - - - +
78G GLY 4.9 9.5 + - - -
80G HIS* 5.7 3.2 + - - -
114G LYS* 3.8 32.3 - - + +
221G SER* 3.2 9.7 + - - +
222G GLU* 1.3 80.4 - - + +
224G ASP* 1.3 61.5 + - - +
226G GLN* 3.3 9.3 + - + +
227G ASP* 2.9 53.5 + - - +
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Residues in contact with ASP 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G THR* 4.2 10.7 - - + -
114G LYS* 3.9 13.5 + - - +
115G GLY* 3.4 30.3 + - - -
219G ALA 3.2 16.3 - - - +
220G VAL* 3.8 11.7 - - + -
221G SER* 2.8 38.0 + - - +
223G LYS* 1.3 76.2 - - - +
225G ILE* 1.3 59.5 + - - +
227G ASP* 3.7 6.6 - - - +
228G LEU* 2.9 40.8 + - + +
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Residues in contact with ILE 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G VAL* 3.7 19.7 - - + +
221G SER 3.0 21.1 + - - +
222G GLU* 3.5 17.9 - - + +
223G LYS 3.3 0.2 - - - -
224G ASP* 1.3 75.9 - - - +
226G GLN* 1.3 70.1 + - - +
228G LEU* 3.6 1.6 + - - +
229G LYS* 3.3 37.4 + - + +
256G VAL* 4.3 26.4 - - + +
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Residues in contact with GLN 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G HIS* 3.5 15.9 - - + +
222G GLU 3.2 17.4 + - - +
223G LYS* 3.6 11.0 - - + +
224G ASP 3.3 0.4 - - - -
225G ILE* 1.3 87.0 - - - +
227G ASP* 1.3 61.6 + - - +
229G LYS* 4.2 7.5 - - - +
230G PHE* 3.3 22.5 + - - +
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Residues in contact with ASP 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G PHE* 3.4 37.1 - - + +
80G HIS* 2.9 26.6 + - - -
111G LEU* 3.5 19.6 - - + +
113G THR* 5.5 4.0 - - + -
114G LYS 4.8 4.7 + - - -
223G LYS* 2.9 47.0 + - - +
224G ASP* 3.3 9.2 + - - +
226G GLN* 1.3 77.5 - - - +
228G LEU* 1.3 60.1 + - - +
230G PHE* 3.5 5.5 - - - +
231G GLY 3.2 15.8 + - - -
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Residues in contact with LEU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G LEU* 4.6 4.5 - - + -
113G THR* 4.6 14.6 - - + -
220G VAL* 4.5 12.6 - - + -
224G ASP* 2.9 24.2 + - + +
225G ILE 4.0 0.2 - - - +
226G GLN 3.3 0.2 - - - -
227G ASP* 1.3 73.4 - - - +
229G LYS* 1.3 59.7 + - - +
230G PHE 3.1 1.3 - - - -
231G GLY* 2.9 17.5 + - - -
232G VAL* 3.0 18.6 + - - +
239G VAL* 3.8 32.1 - - + -
253G VAL* 4.0 23.6 - - + +
256G VAL* 3.8 31.2 - - + -
257G LEU* 3.9 23.5 - - + +
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Residues in contact with LYS 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G ILE* 3.3 28.1 + - + +
226G GLN* 4.2 7.6 - - - +
228G LEU* 1.3 77.8 - - - +
230G PHE* 1.3 61.0 + - - +
232G VAL* 3.3 13.5 + - + +
233G GLU* 3.1 30.8 + - - +
256G VAL* 3.9 26.7 + - + +
257G LEU 5.8 0.2 + - - -
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Residues in contact with PHE 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G PHE* 3.9 36.6 - + - -
80G HIS* 3.4 56.1 - - + -
83G HIS* 4.3 5.6 - - + -
84G ALA* 4.1 9.4 - - + -
87G ILE* 4.6 4.9 - - + -
226G GLN 3.3 17.3 + - - +
227G ASP 3.5 3.8 - - - +
229G LYS* 1.3 77.6 - - - +
231G GLY* 1.3 58.7 + - - +
233G GLU* 3.4 19.5 + - + +
234G GLN* 3.0 71.1 + - + +
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Residues in contact with GLY 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G LEU* 3.7 22.4 - - - -
227G ASP 3.2 7.3 + - - -
228G LEU 2.9 8.8 + - - -
230G PHE* 1.3 74.7 - - - +
232G VAL* 1.3 65.1 + - - +
234G GLN* 4.4 1.8 - - - -
235G ASP 3.1 3.6 + - - -
236G VAL* 3.1 43.9 + - - +
257G LEU* 6.2 0.4 - - - -
264G ILE* 4.9 0.6 - - - +
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Residues in contact with VAL 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU 3.0 18.6 + - - +
229G LYS* 3.5 15.9 - - + +
230G PHE 3.3 0.2 - - - -
231G GLY* 1.3 76.7 - - - +
233G GLU* 1.3 58.2 + - + +
234G GLN 3.2 0.2 - - - -
235G ASP* 3.1 19.6 + - - +
256G VAL 5.5 0.4 - - - +
257G LEU* 3.7 38.1 - - + +
260G LYS* 4.0 32.5 - - + +
261G GLY* 4.5 2.2 - - - +
264G ILE* 4.5 12.2 - - + +
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Residues in contact with GLU 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G LYS* 3.1 18.5 + - - +
230G PHE* 3.4 28.3 + - + +
232G VAL* 1.3 77.3 - - + +
234G GLN* 1.3 63.7 + - + +
235G ASP* 3.3 1.0 - - - +
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Residues in contact with GLN 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G ALA* 4.2 14.9 - - - +
87G ILE* 3.6 37.8 - - + +
91G ARG* 2.9 34.7 + - - -
230G PHE* 3.0 57.2 + - + +
231G GLY* 4.0 6.1 - - - +
232G VAL 3.2 0.2 - - - -
233G GLU* 1.3 81.7 + - + +
235G ASP* 1.3 62.4 + - - +
236G VAL* 4.6 1.9 - - + +
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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