Contacts of the helix formed by residues 213 - 226 (chain A) in PDB entry 1Q2L
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 PRO 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ASP* 3.0 16.8 - - - +
209A LYS 3.3 2.8 - - - +
211A GLY* 3.6 8.3 - - - +
212A ASN* 1.3 93.2 - - - +
214A VAL* 1.3 65.6 + - - +
215A GLN* 4.5 7.9 - - + +
216A GLN* 3.3 20.0 + - + +
217A ALA* 3.2 18.0 + - - +
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Residues in contact with VAL 214 (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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83A TYR* 3.2 39.6 + - + +
86A LEU* 4.2 7.0 - - + -
89A TYR* 3.5 43.1 - - + +
159A ALA* 5.3 8.5 - - + -
206A LEU 4.1 7.0 - - - +
208A ASP* 2.6 30.4 + - + +
213A PRO* 1.3 69.4 - - - +
215A GLN* 1.3 69.5 + - + +
217A ALA* 3.1 2.7 + - - +
218A LEU* 2.9 24.4 + - + +
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Residues in contact with GLN 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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154A LEU 3.0 24.0 + - - +
155A ASP* 3.5 17.4 + - - +
156A LYS* 3.1 40.2 - - + +
208A ASP* 4.5 0.2 + - - -
213A PRO* 3.2 5.9 - - + +
214A VAL* 1.3 84.5 - - + +
216A GLN* 1.3 63.1 + - - +
218A LEU* 3.3 14.6 + - - +
219A LYS* 3.1 43.9 + - - +
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Residues in contact with GLN 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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213A PRO* 3.3 24.7 + - + +
214A VAL 3.3 0.2 - - - -
215A GLN* 1.3 77.6 - - - +
217A ALA* 1.3 60.1 + - - +
219A LYS* 3.3 23.3 + - - +
220A ASP* 2.8 63.9 + - - +
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Residues in contact with ALA 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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80A PRO* 5.4 3.6 - - + -
83A TYR* 3.9 27.6 - - + -
86A LEU* 3.7 16.1 - - + +
212A ASN* 5.1 4.9 + - - +
213A PRO 3.2 12.2 + - - +
214A VAL* 3.1 9.5 + - - +
216A GLN* 1.3 77.3 - - - +
218A LEU* 1.3 57.8 + - - +
220A ASP* 3.3 8.1 + - - +
221A PHE* 2.9 31.7 + - - +
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Residues in contact with LEU 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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86A LEU* 3.8 20.6 - - + +
89A TYR* 3.9 25.8 - - + -
90A LEU* 3.7 46.1 - - + +
93A MET* 4.0 24.2 - - + -
154A LEU* 4.2 17.3 - - + +
159A ALA* 6.1 1.1 - - + -
214A VAL* 2.9 19.9 + - + +
215A GLN* 3.4 15.0 - - - +
217A ALA* 1.3 77.5 - - - +
219A LYS* 1.3 57.8 + - - +
221A PHE* 3.3 4.3 + - - +
222A HIS* 2.9 30.0 + - - +
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Residues in contact with LYS 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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153A LEU 3.3 24.0 + - - -
154A LEU* 3.6 25.1 + - + +
155A ASP* 5.1 1.6 + - - -
215A GLN* 3.1 39.9 + - - +
216A GLN* 3.7 32.1 - - - +
218A LEU* 1.3 79.8 - - - +
220A ASP* 1.3 57.4 + - - +
222A HIS* 3.4 2.6 + - - +
223A GLU* 2.9 30.5 + - - +
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Residues in contact with ASP 220 (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 GLN* 2.8 56.4 + - - +
217A ALA* 3.7 7.6 - - - +
219A LYS* 1.3 70.6 - - - +
221A PHE* 1.3 61.0 + - - +
223A GLU* 3.3 5.4 + - - +
224A LYS* 2.9 33.6 + - + +
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Residues in contact with PHE 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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74A VAL* 3.8 22.2 - - + -
75A GLY 4.0 3.6 - - - -
78A GLU* 3.4 28.0 - - + -
79A ASP* 4.0 7.9 - - - -
80A PRO* 4.3 5.6 - - + -
86A LEU* 3.7 22.9 - - + -
87A ALA* 3.9 29.4 - - + -
90A LEU* 3.9 20.4 - - + -
127A THR* 5.8 0.7 - - - -
217A ALA 2.9 17.7 + - - +
218A LEU* 3.6 4.5 - - - +
220A ASP* 1.3 76.6 - - - +
222A HIS* 1.3 58.3 + - - +
224A LYS* 3.2 4.7 + - - -
225A TYR* 2.8 61.2 + + + +
226A TYR* 4.7 8.3 - + - -
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Residues in contact with HIS 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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90A LEU* 4.0 16.1 - - + +
94A SER* 4.8 0.6 + - - -
148A ALA 4.7 0.4 - - - -
149A ILE 3.0 29.9 + - - -
150A ALA 4.1 6.9 + - - -
152A PRO* 3.5 33.9 - - + +
154A LEU* 4.3 9.2 - - + -
218A LEU 2.9 18.1 + - - +
219A LYS 3.6 4.9 - - - +
221A PHE* 1.3 76.7 - - - +
223A GLU* 1.3 59.3 + - - +
226A TYR* 2.9 57.8 + + + +
256A PRO* 6.0 1.0 - - - +
258A LYS* 3.0 21.3 + - - -
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Residues in contact with GLU 223 (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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219A LYS 2.9 17.9 + - - +
220A ASP* 3.7 6.7 - - - +
222A HIS* 1.3 78.4 - - - +
224A LYS* 1.3 62.3 + - - +
258A LYS* 3.0 54.1 + - - +
260A SER* 4.6 0.5 + - - -
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Residues in contact with LYS 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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220A ASP* 2.9 18.8 + - + +
221A PHE* 3.6 4.7 - - - +
223A GLU* 1.3 80.1 - - - +
225A TYR* 1.3 101.8 + - + +
260A SER* 3.3 24.0 + - - -
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Residues in contact with TYR 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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72A VAL* 3.7 12.3 - - - +
74A VAL* 3.6 30.4 - - + +
78A GLU* 3.1 30.2 + - + +
221A PHE* 2.8 66.4 + + + +
224A LYS* 1.3 118.6 - - + +
226A TYR* 1.3 67.4 + - + +
227A SER* 2.9 12.3 + - - +
230A LEU* 4.4 11.1 - - - +
260A SER* 5.0 2.0 - - - -
261A LYS 5.4 2.7 - - - -
263A PRO* 3.6 24.0 - - + -
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Residues in contact with TYR 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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72A VAL* 4.1 21.5 - - + -
74A VAL* 5.8 0.9 - - + -
87A ALA 4.7 1.7 + - - -
90A LEU* 3.5 31.6 - - + +
91A GLU 4.4 2.8 + - - -
94A SER* 4.2 9.4 - - - -
127A THR* 3.6 17.3 + - - +
129A PHE* 3.6 32.4 - + - -
149A ILE* 4.2 16.3 - - + +
221A PHE* 4.7 11.2 - + - -
222A HIS* 2.9 56.4 + + + +
224A LYS 4.0 0.2 - - - -
225A TYR* 1.3 76.0 - - + +
227A SER* 1.3 54.7 + - - +
228A ALA 4.2 0.5 + - - -
231A MET* 3.3 27.6 - - + +
255A VAL* 4.7 3.5 - - - +
256A PRO* 4.4 4.5 - - - +
258A LYS* 3.4 17.7 + - - -
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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