Contacts of the helix formed by residues 225 - 242 (chain A) in PDB entry 3N7T
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 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.2 0.2 - - - -
208A ASP 3.4 1.4 + - - -
209A ASP* 3.5 8.7 - - - -
210A PHE 2.9 32.5 + - - -
211A CYS* 3.7 2.0 - - - -
220A GLY* 4.0 0.9 - - - -
221A ALA 3.4 18.6 + - - -
222A ASN* 2.7 28.9 + - - -
224A GLN* 1.3 76.7 - - - +
226A ALA* 1.3 56.2 + - - +
227A THR 3.4 1.8 - - - -
228A ASN 3.4 3.2 + - - -
229A THR* 2.6 41.7 + - - -
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER 4.5 3.1 - - - +
32A GLU* 4.2 32.3 - - + -
35A HIS* 4.6 1.3 - - + +
36A PRO* 4.1 16.0 - - + +
106A PHE* 4.2 0.3 - - - -
140A VAL* 3.9 16.8 - - + -
222A ASN 3.6 1.6 + - - -
223A PRO 3.2 15.3 + - - +
225A SER* 1.3 77.0 - - - +
227A THR* 1.3 63.9 + - - +
229A THR* 3.4 2.6 + - - -
230A ALA* 3.0 24.3 + - - +
244A EDO 3.3 3.5 + - - +
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Residues in contact with THR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 3.4 23.7 - - - +
39A GLU* 3.5 27.3 + - - +
224A GLN 5.8 0.2 - - - -
226A ALA* 1.3 74.0 - - - +
228A ASN* 1.3 61.1 + - - +
230A ALA* 3.3 5.1 + - - +
231A ARG* 2.9 53.2 + - - +
244A EDO 3.1 34.7 + - - +
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Residues in contact with ASN 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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209A ASP* 2.8 33.2 + - - +
211A CYS* 3.7 18.2 - - + -
224A GLN 5.6 0.2 + - - -
225A SER 3.4 2.2 + - - +
226A ALA 3.4 0.4 - - - -
227A THR* 1.3 81.9 - - - +
229A THR* 1.3 58.5 + - - +
231A ARG* 3.8 26.2 + - - +
232A ASP* 2.9 38.0 + - - +
235A LYS* 6.0 0.2 + - - -
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.8 18.2 - - + -
139A ALA 3.8 18.4 - - - +
140A VAL* 3.9 2.8 - - - +
211A CYS* 3.4 7.9 - - - -
218A VAL* 3.6 13.4 - - + +
219A THR 3.8 5.6 - - - -
220A GLY* 3.2 37.4 - - - +
225A SER 2.6 30.4 + - - -
226A ALA 3.7 4.9 - - - -
228A ASN* 1.3 72.6 - - - +
230A ALA* 1.3 54.8 + - - +
233A THR* 2.7 37.9 + - - +
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Residues in contact with ALA 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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36A PRO* 3.7 29.2 - - + +
39A GLU* 4.0 12.8 - - + -
40A LEU* 5.4 3.7 - - + +
106A PHE* 3.6 18.7 - - + -
226A ALA 3.0 13.4 + - - +
227A THR 3.6 7.6 - - - +
229A THR* 1.3 77.0 - - - +
231A ARG* 1.3 56.4 + - - +
233A THR* 3.2 2.9 + - - -
234A ILE* 2.9 38.0 + - + +
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Residues in contact with ARG 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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39A GLU* 2.9 43.0 + - + +
227A THR* 2.9 31.9 + - - +
228A ASN* 3.8 24.5 + - - +
229A THR 3.4 0.2 - - - -
230A ALA* 1.3 76.1 - - - +
232A ASP* 1.3 58.3 + - - +
234A ILE* 3.3 10.7 + - + +
235A LYS* 2.9 43.6 + - - +
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Residues in contact with ASP 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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211A CYS* 3.6 22.7 - - - +
213A VAL* 3.5 22.0 - - + +
218A VAL* 3.6 19.1 - - + -
228A ASN* 2.9 25.5 + - - +
231A ARG* 1.3 71.4 - - - +
233A THR* 1.3 65.3 + - - +
235A LYS* 3.3 27.1 + - - +
236A VAL* 3.0 27.5 + - - +
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Residues in contact with THR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 6.1 0.7 - - + -
104A LEU* 3.8 27.6 - - + -
105A MET 4.6 0.2 - - - +
106A PHE* 4.2 5.6 - - + -
136A VAL* 3.6 21.5 - - + +
138A GLY* 3.4 30.7 - - - +
218A VAL* 3.5 13.9 - - - +
229A THR 2.7 23.6 + - - -
230A ALA* 3.5 8.3 - - - -
232A ASP* 1.3 77.0 - - - +
234A ILE* 1.3 62.3 + - - +
236A VAL* 3.4 4.3 + - - +
237A TYR* 3.1 21.5 + - - +
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Residues in contact with ILE 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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39A GLU* 3.5 40.8 - - + +
40A LEU* 3.9 24.9 - - + +
43A ALA* 3.9 23.3 - - + -
45A PHE* 4.2 10.3 - - + -
104A LEU* 4.7 2.2 - - + -
230A ALA 2.9 22.7 + - - +
231A ARG* 3.6 8.5 - - + +
232A ASP 3.3 0.2 - - - -
233A THR* 1.3 73.3 - - - +
235A LYS* 1.3 60.5 + - + +
237A TYR* 3.3 7.6 + - - +
238A GLU* 2.9 50.5 + - + +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASN* 6.0 0.2 + - - -
231A ARG* 2.9 29.1 + - - +
232A ASP* 3.3 26.5 + - - +
234A ILE* 1.3 77.1 - - + +
236A VAL* 1.3 63.2 + - + +
238A GLU* 3.4 8.3 + - - +
239A GLY* 3.2 18.2 + - - -
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Residues in contact with VAL 236 (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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136A VAL* 3.6 26.0 - - + -
213A VAL* 3.9 28.9 - - + -
215A GLY 3.8 15.7 - - - +
216A ARG* 4.2 5.8 - - + -
218A VAL* 3.9 9.2 - - + -
232A ASP 3.0 19.0 + - - +
233A THR 3.7 6.3 - - - +
234A ILE 3.3 0.2 - - - -
235A LYS* 1.3 77.0 - - + +
237A TYR* 1.3 61.4 + - - +
239A GLY* 3.3 4.2 + - - -
240A ILE* 3.3 28.6 + - + +
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Residues in contact with TYR 237 (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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4A LEU* 2.8 41.5 + - + -
5A PRO 3.2 19.9 + - - -
6A ARG* 3.3 33.2 + - - +
45A PHE* 3.5 34.1 - + - -
103A GLY 4.0 17.3 - - - -
104A LEU* 4.2 12.8 - - + -
136A VAL* 3.8 12.5 - - + +
233A THR 3.1 14.0 + - - +
234A ILE* 3.5 7.9 - - - +
236A VAL* 1.3 75.7 - - - +
238A GLU* 1.3 72.4 + - - +
240A ILE* 3.1 6.7 + - - +
241A VAL* 3.1 39.2 + - + +
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Residues in contact with GLU 238 (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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6A ARG* 2.9 44.3 + - - -
43A ALA* 4.8 3.1 - - - +
234A ILE* 2.9 39.7 + - + +
235A LYS* 3.8 8.5 - - - +
236A VAL 3.3 0.2 - - - -
237A TYR* 1.3 75.6 - - - +
239A GLY* 1.3 60.5 + - - +
241A VAL* 3.6 6.7 - - - +
242A ASN* 2.6 39.8 + - - +
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Residues in contact with GLY 239 (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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235A LYS 3.2 13.1 + - - -
236A VAL 3.3 4.4 + - - -
237A TYR 3.2 0.2 - - - -
238A GLU* 1.3 77.7 - - - +
240A ILE* 1.3 60.9 + - - +
242A ASN* 3.5 6.2 + - - +
243A GLU* 3.5 21.9 + - - +
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Residues in contact with ILE 240 (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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4A LEU* 3.7 24.7 - - + -
134A GLY* 3.4 24.0 - - - +
136A VAL* 3.6 30.1 - - + -
216A ARG* 3.6 19.5 - - + -
236A VAL* 3.3 13.5 + - + +
237A TYR* 3.1 7.8 + - - +
239A GLY* 1.3 76.8 - - - +
241A VAL* 1.3 64.3 + - + +
243A GLU* 3.2 43.1 + - - +
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Residues in contact with VAL 241 (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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4A LEU* 4.2 22.7 - - + +
6A ARG* 4.3 6.3 - - - +
237A TYR* 3.1 55.6 + - + +
238A GLU* 3.6 19.3 - - - +
240A ILE* 1.3 76.2 - - + +
242A ASN* 1.3 67.6 + - - +
243A GLU* 3.4 2.8 + - - +
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Residues in contact with ASN 242 (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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238A GLU* 2.6 37.6 + - - +
239A GLY* 3.5 7.2 + - - +
240A ILE 3.2 1.4 - - - -
241A VAL* 1.3 88.1 - - - +
243A GLU* 1.3 66.0 + - - +
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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