Contacts of the helix formed by residues 214 - 228 (chain A) in PDB entry 3T3Q
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 THR 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR 4.5 2.5 - - - -
52A GLU* 5.1 0.9 - - - -
210A GLN* 3.5 16.8 - - + +
211A PHE* 2.6 30.6 + - + +
213A SER* 1.3 80.8 - - - +
215A SER* 1.3 65.5 + - - +
216A THR* 3.7 5.3 + - - -
217A GLY 3.2 10.6 + - - -
218A GLN* 3.0 23.9 + - - +
477A HIS* 3.8 33.9 - - + +
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Residues in contact with SER 215 (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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51A THR* 2.8 38.2 + - - -
52A GLU* 3.6 27.8 + - - +
214A THR* 1.3 74.8 - - - +
216A THR* 1.3 59.4 + - - +
219A LEU* 3.0 28.1 + - - +
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Residues in contact with THR 216 (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 PHE* 3.9 20.4 - - + -
214A THR* 3.3 4.3 + - - -
215A SER* 1.3 76.4 - - - +
217A GLY* 1.3 55.5 + - - +
219A LEU* 3.3 10.1 + - + +
220A TYR* 2.8 33.4 + - - +
227A MET* 3.8 20.3 - - + +
233A PRO* 4.3 19.1 - - + +
234A GLN* 3.9 13.2 - - - +
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Residues in contact with GLY 217 (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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104A GLN* 5.4 0.3 + - - -
106A THR* 4.6 1.6 + - - -
211A PHE* 3.3 39.8 - - - -
212A THR* 4.3 4.3 - - - -
214A THR* 3.2 9.5 + - - -
216A THR* 1.3 79.8 - - - +
218A GLN* 1.3 59.4 + - - +
220A TYR* 3.3 17.0 - - - +
221A GLU* 3.3 17.0 + - - +
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Residues in contact with GLN 218 (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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51A THR* 3.3 26.0 - - - +
54A MET* 3.2 32.7 - - + +
104A GLN* 4.6 1.6 - - - +
212A THR 3.2 20.4 + - - +
214A THR 3.0 15.1 + - - +
217A GLY* 1.3 73.6 + - - +
219A LEU* 1.3 66.2 + - - +
220A TYR 3.2 0.2 - - - -
221A GLU* 3.3 35.7 + - - +
222A MET* 3.6 11.8 + - - +
368A MET* 3.3 14.0 - - - +
392A TYR* 5.2 3.1 + - - -
479A GLY* 3.7 24.0 - - - -
480A PHE* 3.4 13.5 - - - +
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Residues in contact with LEU 219 (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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46A TYR* 4.1 15.0 - - + +
51A THR* 3.9 23.8 - - + +
215A SER 3.0 18.8 + - - +
216A THR* 3.5 10.3 - - + +
218A GLN* 1.3 76.8 - - - +
220A TYR* 1.3 56.2 + - - +
222A MET* 2.9 22.4 + - - +
223A PHE* 2.9 41.2 + - + +
227A MET* 3.9 22.7 - - + -
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Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ALA* 3.6 28.4 + - + -
106A THR* 3.4 22.7 - - - -
109A TRP* 4.3 5.0 - - - +
211A PHE* 4.4 6.7 - + + -
216A THR 2.8 17.6 + - - +
217A GLY* 3.3 14.6 - - - +
218A GLN 3.2 0.4 - - - -
219A LEU* 1.3 73.6 - - - +
221A GLU* 1.3 56.2 + - - +
224A SER* 3.0 52.9 + - - -
227A MET* 3.5 28.0 - - + -
228A LYS* 3.3 40.1 + - - +
234A GLN* 3.7 12.3 - - + -
238A PHE* 3.2 30.8 - + - -
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Residues in contact with GLU 221 (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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73A LEU* 4.2 4.3 - - + +
76A ARG* 2.8 54.7 + - - +
104A GLN* 3.0 29.2 + - - +
105A ALA* 2.7 36.7 + - - +
106A THR* 3.3 15.2 + - - -
217A GLY 3.3 12.6 + - - +
218A GLN* 3.5 31.0 - - - +
219A LEU 3.2 0.6 - - - -
220A TYR* 1.3 74.7 - - - +
222A MET* 1.3 60.4 + - + +
224A SER* 4.9 2.0 + - - -
392A TYR* 4.5 11.0 + - - +
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Residues in contact with MET 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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43A ILE 3.7 14.6 - - - +
46A TYR* 3.9 22.2 - - + +
49A LEU* 4.4 14.1 - - + +
51A THR* 4.0 26.2 - - - -
54A MET* 5.3 3.6 - - - +
73A LEU* 3.5 29.7 - - + +
74A GLY 3.4 20.6 - - - +
75A PRO* 3.3 28.2 - - - +
76A ARG* 5.7 0.3 - - - +
218A GLN 3.7 9.6 - - - +
219A LEU* 2.9 9.1 + - - +
221A GLU* 1.3 80.7 - - + +
223A PHE* 1.3 82.4 + - + +
224A SER 3.8 1.3 - - - -
225A SER* 5.5 0.2 + - - -
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.7 51.4 - + + -
43A ILE* 3.8 21.8 - - + -
46A TYR* 3.8 26.5 - + - -
74A GLY* 3.9 4.5 - - - -
75A PRO* 5.5 0.2 - - - -
219A LEU* 2.9 35.0 + - + +
220A TYR 3.8 1.3 - - - -
222A MET* 1.3 102.9 - - + +
224A SER* 1.3 59.3 + - - +
225A SER* 3.2 7.4 - - - -
226A VAL* 3.1 11.1 + - + -
227A MET* 3.0 38.6 + - + +
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Residues in contact with SER 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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103A GLU* 4.9 3.8 + - - -
105A ALA* 3.9 13.8 - - - +
220A TYR* 3.0 50.7 + - - -
221A GLU 5.2 1.6 + - - -
222A MET 3.8 1.4 + - - -
223A PHE* 1.3 76.4 - - - +
225A SER* 1.3 59.5 + - - +
228A LYS* 3.0 40.8 + - - +
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Residues in contact with SER 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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42A PHE* 4.3 13.9 - - - -
75A PRO* 5.2 5.7 - - - +
222A MET 5.5 0.2 + - - -
223A PHE* 4.4 4.3 - - - -
224A SER* 1.3 78.0 + - - +
226A VAL* 1.3 62.7 + - - +
228A LYS* 4.6 8.0 - - - +
229A HIS* 3.8 13.9 + - - -
42B PHE* 3.8 8.1 - - - -
75B PRO* 5.5 0.9 - - - +
225B SER* 3.6 41.9 + - - -
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Residues in contact with VAL 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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42A PHE* 4.1 15.9 - - + -
223A PHE* 3.1 10.2 + - + +
224A SER 3.0 0.2 - - - -
225A SER* 1.3 80.3 - - - +
227A MET* 1.3 66.8 + - + +
228A LYS 3.3 2.2 - - - -
229A HIS* 3.1 18.9 + - - +
230A LEU* 3.6 30.6 + - + +
42B PHE* 4.0 25.6 - - + -
226B VAL* 3.5 31.4 - - + -
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Residues in contact with MET 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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216A THR* 3.8 38.1 - - + +
219A LEU* 3.9 28.3 - - + +
220A TYR* 3.5 35.7 - - + +
223A PHE* 3.0 25.2 + - + +
226A VAL* 1.3 76.5 - - + +
228A LYS* 1.3 59.8 + - - +
229A HIS 3.0 7.0 + - - -
230A LEU* 3.1 21.8 + - + +
234A GLN* 3.0 40.7 + - + +
235A GLN* 3.9 1.9 + - - -
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Residues in contact with LYS 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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108A ASP* 5.5 4.4 + - - -
109A TRP* 4.7 16.4 + - + +
220A TYR* 3.3 28.3 + - - +
224A SER* 3.0 24.6 + - - +
225A SER* 4.6 6.3 - - - +
227A MET* 1.3 75.3 - - - +
229A HIS* 1.3 94.7 + - + +
230A LEU 3.5 0.2 - - - -
235A GLN* 3.1 16.8 + - - +
238A PHE* 4.1 12.2 - - + -
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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