Contacts of the helix formed by residues 221 - 235 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLY 5.0 5.0 + - - -
116A PRO* 6.4 0.7 - - - -
218A PRO* 4.4 18.6 - - - -
219A ALA 3.8 1.0 + - - -
220A VAL* 1.3 75.1 - - - +
222A GLU* 1.3 71.8 + - - +
223A LYS* 3.5 9.1 + - - +
224A ASP* 2.8 36.1 + - - -
225A ILE* 3.0 30.3 + - - +
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Residues in contact with GLU 222 (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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218A PRO* 5.8 0.7 - - - +
221A SER* 1.3 80.4 - - - +
223A LYS* 1.3 69.7 + - - +
225A ILE* 3.5 16.6 + - + +
226A GLN* 3.1 31.2 + - - +
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Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 3.4 26.1 + - - +
76A SER* 5.2 3.1 + - - +
78A GLY 4.9 9.9 + - - -
80A HIS* 5.9 2.2 + - - -
114A LYS* 3.6 33.2 - - + +
221A SER* 3.2 8.4 - - - +
222A GLU* 1.3 87.1 - - - +
224A ASP* 1.3 61.2 + - - +
226A GLN* 3.3 9.2 + - + +
227A ASP* 2.9 47.9 + - - +
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Residues in contact with ASP 224 (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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113A THR* 4.0 10.9 - - + +
114A LYS* 3.9 12.1 + - - +
115A GLY* 3.2 31.2 + - - -
218A PRO 4.9 0.2 - - - +
219A ALA 3.2 15.2 - - - +
220A VAL* 3.7 12.3 - - + -
221A SER* 2.8 38.4 + - - +
223A LYS* 1.3 76.9 - - - +
225A ILE* 1.3 58.5 + - - +
227A ASP* 3.4 7.8 + - - +
228A LEU* 3.0 39.2 + - + +
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Residues in contact with ILE 225 (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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220A VAL* 3.7 17.0 - - + +
221A SER 3.0 17.8 + - - +
222A GLU* 3.6 17.9 - - + +
224A ASP* 1.3 75.9 - - - +
226A GLN* 1.3 63.7 + - + +
228A LEU* 3.4 1.4 + - - +
229A LYS* 3.1 51.8 + - - +
256A VAL* 4.4 21.5 - - + +
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Residues in contact with GLN 226 (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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80A HIS* 3.5 20.8 - - + +
222A GLU* 3.1 18.4 + - + +
223A LYS* 3.3 12.1 + - + +
225A ILE* 1.3 78.6 - - - +
227A ASP* 1.3 62.1 + - - +
229A LYS* 3.6 8.3 + - - +
230A PHE* 3.2 23.7 + - - +
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Residues in contact with ASP 227 (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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75A PHE* 3.4 46.7 - - + +
80A HIS* 3.4 17.8 + - - -
111A LEU* 3.2 23.6 - - + +
113A THR* 4.6 3.9 - - + -
114A LYS 4.2 8.1 + - - -
223A LYS* 2.9 40.2 + - - +
224A ASP* 3.6 9.0 - - - +
226A GLN* 1.3 76.3 - - - +
228A LEU* 1.3 57.3 + - - +
230A PHE* 3.4 4.6 + - - +
231A GLY 3.0 21.1 + - - -
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Residues in contact with LEU 228 (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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111A LEU* 4.8 2.2 - - + -
113A THR* 4.5 12.8 - - + -
220A VAL* 4.6 10.8 - - + -
224A ASP* 3.0 27.6 + - + +
226A GLN 3.3 0.2 - - - -
227A ASP* 1.3 74.1 - - - +
229A LYS* 1.3 61.4 + - - +
231A GLY* 2.9 18.0 + - - +
232A VAL* 3.2 17.9 + - - +
239A VAL* 3.8 39.7 - - + -
253A VAL* 4.1 24.0 - - + -
256A VAL* 3.7 33.4 - - + -
257A LEU* 3.9 16.9 - - + +
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Residues in contact with LYS 229 (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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225A ILE* 3.1 40.3 + - + +
226A GLN* 4.0 8.3 - - - +
228A LEU* 1.3 75.1 - - - +
230A PHE* 1.3 58.4 + - - +
232A VAL* 3.1 23.7 + - - +
233A GLU* 3.4 18.5 + - - +
256A VAL* 4.6 20.4 + - + +
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Residues in contact with PHE 230 (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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75A PHE* 4.0 32.8 - + - -
80A HIS* 3.3 54.5 - - + +
83A HIS* 4.3 9.0 - - + -
84A ALA* 3.7 14.6 - - + -
87A ILE* 4.4 4.3 - - + -
111A LEU* 5.1 0.4 - - + -
226A GLN 3.2 16.3 + - - +
227A ASP 3.5 2.9 - - - +
228A LEU 3.2 0.2 - - - -
229A LYS* 1.3 77.3 - - - +
231A GLY* 1.3 61.7 + - - +
232A VAL 3.3 0.2 - - - -
233A GLU* 3.9 20.4 - - - +
234A GLN* 3.2 55.2 + - + +
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Residues in contact with GLY 231 (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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111A LEU* 3.6 22.7 - - - -
227A ASP 3.0 6.7 + - - -
228A LEU 2.9 11.5 + - - -
230A PHE* 1.3 77.7 - - - +
232A VAL* 1.3 56.5 + - - +
234A GLN* 4.7 0.2 - - - -
235A ASP 3.1 5.0 + - - -
236A VAL* 3.0 46.4 + - - +
239A VAL* 6.1 0.7 - - - -
257A LEU* 5.8 0.4 - - - -
264A ILE* 4.5 1.2 - - - +
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Residues in contact with VAL 232 (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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228A LEU 3.4 14.4 - - - +
229A LYS* 3.1 12.9 + - - +
231A GLY* 1.3 76.0 - - - +
233A GLU* 1.3 61.8 + - - +
235A ASP* 3.1 20.8 + - - +
256A VAL 5.6 0.7 - - - +
257A LEU* 3.8 32.8 - - + +
260A LYS* 3.5 44.6 - - + +
261A GLY* 4.5 1.1 - - - -
264A ILE* 4.2 10.8 - - + -
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Residues in contact with GLU 233 (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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229A LYS* 3.4 15.2 + - - +
230A PHE* 3.9 24.5 - - + +
232A VAL* 1.3 74.4 - - - +
234A GLN* 1.3 72.4 + - + +
235A ASP* 3.1 5.5 + - - +
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Residues in contact with GLN 234 (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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84A ALA* 3.6 27.0 - - - +
87A ILE* 3.7 27.3 - - + +
91A ARG* 2.6 42.2 + - - +
230A PHE* 3.2 57.9 + - + +
231A GLY 4.2 3.1 - - - +
233A GLU* 1.3 80.4 + - - +
235A ASP* 1.3 59.1 + - - +
236A VAL* 3.5 4.5 - - + -
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Residues in contact with ASP 235 (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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91A ARG* 3.3 15.1 + - - +
231A GLY 3.1 5.0 + - - -
232A VAL* 3.1 16.1 + - - +
233A GLU 4.4 3.6 - - - +
234A GLN* 1.3 84.3 - - - +
236A VAL* 1.3 70.7 + - - +
237A ASP* 3.6 9.0 - - - +
264A ILE* 5.9 0.9 - - - -
457A GLN* 5.1 9.0 + - - -
460A ARG* 4.2 17.0 + - - -
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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