Contacts of the helix formed by residues 210 - 224 (chain A) in PDB entry 2Z9I
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 VAL 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 6.1 0.4 - - + -
105A LEU* 4.1 25.4 - - + -
106A GLY 3.5 21.1 - - - +
108A SER* 3.7 16.8 + - - +
180A LEU* 3.6 42.0 - - + +
181A VAL* 3.0 26.8 + - - +
182A GLY* 4.4 1.3 - - - +
208A ILE 3.4 1.7 + - - -
209A PRO* 1.3 71.1 - - - +
211A ASP* 1.3 61.5 + - - +
213A ALA* 4.2 6.7 - - + -
214A LYS* 2.8 39.0 + - + +
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Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLY 4.2 2.3 - - - +
107A SER* 3.7 14.4 + - - -
108A SER* 3.0 35.0 + - - +
109A SER* 3.6 20.4 + - - -
209A PRO* 5.2 1.1 - - + -
210A VAL* 1.3 77.1 - - - +
212A GLN* 1.3 62.7 + - + +
214A LYS* 4.0 7.8 - - - +
215A ARG* 3.2 21.5 + - - +
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Residues in contact with GLN 212 (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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156A ASP* 3.1 39.9 + - - +
208A ILE* 4.1 10.6 - - + +
209A PRO* 3.2 35.0 + - - +
211A ASP* 1.3 75.2 - - + +
213A ALA* 1.3 66.7 + - - +
215A ARG* 3.2 20.4 + - - +
216A ILE* 3.2 26.8 + - + +
285A ARG 4.3 6.2 - - - +
286A SER* 3.6 36.2 + - - +
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Residues in contact with ALA 213 (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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45A LEU* 4.2 9.8 - - + +
89A ILE* 3.8 34.6 - - + +
183A VAL* 3.8 20.4 - - + -
208A ILE* 4.0 3.7 - - + +
209A PRO 3.0 15.6 + - - +
210A VAL* 3.8 7.9 - - + +
212A GLN* 1.3 74.7 - - - +
214A LYS* 1.3 58.4 + - - +
216A ILE* 3.5 1.7 + - - +
217A ALA* 2.8 31.8 + - - +
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Residues in contact with LYS 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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45A LEU* 5.8 2.2 - - - -
105A LEU* 3.4 39.3 - - + +
106A GLY 6.0 1.1 - - - +
210A VAL* 2.8 24.5 + - + +
211A ASP* 4.0 6.7 - - - +
213A ALA* 1.3 72.5 - - - +
215A ARG* 1.3 68.5 + - + +
217A ALA* 3.9 5.1 - - - +
218A ASP* 3.0 45.2 + - - +
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Residues in contact with ARG 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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211A ASP 3.2 16.9 + - - +
212A GLN* 3.2 10.2 + - - +
214A LYS* 1.3 80.5 - - - +
216A ILE* 1.3 83.3 + - - +
218A ASP* 3.4 5.4 + - - +
219A GLU* 3.2 45.0 + - + +
227A SER 3.2 25.5 + - - -
228A HIS* 5.3 4.0 + - - +
285A ARG 4.1 12.1 + - - -
286A SER 5.0 4.0 + - - -
287A LYS 3.5 17.8 + - - -
288A ALA* 3.5 32.9 - - - +
289A PRO* 4.0 8.1 - - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 3.8 4.7 - - + +
87A SER* 3.1 47.1 - - - +
89A ILE* 3.6 19.3 - - + -
208A ILE* 6.2 0.4 - - + -
212A GLN* 3.2 24.1 + - + +
213A ALA 4.0 2.5 - - - +
215A ARG* 1.3 98.3 - - - +
217A ALA* 1.3 58.6 + - - +
219A GLU* 3.2 9.3 + - - +
220A LEU* 2.8 36.8 + - + +
226A ALA* 3.7 22.0 - - + -
227A SER 5.3 1.3 - - - +
228A HIS* 5.4 2.9 - - - +
285A ARG 5.8 2.0 - - - +
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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
----------------------------------------------------------
38A LEU* 4.2 13.9 - - + -
45A LEU* 3.7 23.6 - - + -
89A ILE* 4.0 2.4 - - - +
91A VAL* 3.7 17.7 - - + -
213A ALA 2.8 22.8 + - - +
214A LYS* 3.9 5.8 - - - +
216A ILE* 1.3 73.0 - - - +
218A ASP* 1.3 57.4 + - - +
220A LEU* 3.3 2.4 + - - +
221A ILE* 2.8 37.2 + - + +
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Residues in contact with ASP 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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38A LEU* 5.9 0.9 - - - +
214A LYS* 3.0 46.8 + - - +
215A ARG* 3.7 5.1 - - - +
217A ALA* 1.3 76.7 - - - +
219A GLU* 1.3 58.5 + - + +
221A ILE* 3.5 13.9 + - - +
222A SER* 3.1 30.7 + - - -
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Residues in contact with GLU 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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215A ARG* 3.2 44.2 + - - +
216A ILE* 3.2 6.8 + - - +
218A ASP* 1.3 74.4 - - + +
220A LEU* 1.3 57.8 + - - +
222A SER* 3.7 4.9 + - - -
223A THR* 2.8 32.1 + - - -
224A GLY 3.3 3.5 + - - -
225A LYS 3.5 12.8 - - - +
226A ALA* 3.2 6.6 - - - +
227A SER* 2.8 43.0 + - - +
289A PRO* 5.1 1.9 - - - +
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Residues in contact with LEU 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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81A VAL* 3.9 11.6 - - - +
82A GLY* 3.6 23.6 - - - +
83A ALA 3.9 18.6 - - - +
84A ASP* 4.2 1.8 - - + +
89A ILE* 3.8 21.5 - - + +
90A ALA* 3.9 7.4 - - - -
91A VAL* 4.1 13.9 - - + +
216A ILE* 2.8 37.4 + - + +
217A ALA 3.6 3.6 - - - +
219A GLU* 1.3 71.6 - - - +
221A ILE* 1.3 60.4 + - - +
224A GLY* 3.0 45.0 + - - +
225A LYS* 3.8 15.5 - - - -
226A ALA* 3.9 6.7 - - + +
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Residues in contact with ILE 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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38A LEU* 4.2 20.6 - - + -
43A LEU* 3.7 36.1 - - + -
81A VAL* 4.3 10.5 - - + +
91A VAL* 3.9 21.1 - - + -
217A ALA 2.8 29.8 + - - +
218A ASP* 3.7 15.0 - - - +
220A LEU* 1.3 76.0 - - - +
222A SER* 1.3 62.3 + - - +
224A GLY 4.8 0.2 + - - -
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Residues in contact with SER 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 ASP 3.1 18.0 + - - -
219A GLU* 3.7 5.9 + - - +
221A ILE* 1.3 79.4 - - - +
223A THR* 1.3 61.3 + - - +
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Residues in contact with THR 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 GLU 2.8 16.7 + - - -
222A SER* 1.3 76.9 + - - +
224A GLY* 1.3 56.0 + - - +
225A LYS 3.2 10.0 + - - -
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Residues in contact with GLY 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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81A VAL 4.4 10.0 - - - +
82A GLY* 4.0 9.4 - - - -
83A ALA 4.7 1.9 + - - +
219A GLU 3.3 1.2 + - - -
220A LEU* 3.0 33.6 + - - +
221A ILE 4.8 0.2 + - - -
222A SER 3.9 0.4 - - - -
223A THR* 1.3 75.6 - - - +
225A LYS* 1.3 55.1 + - - +
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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