Contacts of the helix formed by residues 210 - 223 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C LEU* 6.1 0.2 - - + -
105C LEU* 3.8 28.0 - - + -
106C GLY 3.2 25.4 - - - +
108C SER 3.5 18.8 - - - +
180C LEU* 3.6 28.3 - - + +
181C VAL* 2.9 26.3 + - - +
182C GLY* 4.2 2.7 - - - +
208C ILE 3.5 2.5 + - - -
209C PRO* 1.3 72.1 - - - +
211C ASP* 1.3 61.2 + - - +
213C ALA* 4.2 7.4 - - + -
214C LYS* 2.8 36.2 + - + +
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Residues in contact with ASP 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLY 4.1 2.3 - - - +
107C SER* 3.7 11.8 + - - -
108C SER* 3.1 33.3 + - - +
109C SER* 3.4 25.5 + - - -
209C PRO* 3.2 1.9 + - + -
210C VAL* 1.3 76.9 - - - +
212C GLN* 1.3 63.2 + - + +
214C LYS* 4.1 5.0 - - - +
215C ARG* 3.2 23.4 + - - +
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Residues in contact with GLN 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ASN* 5.4 0.2 - - - +
155C LEU* 5.8 0.2 - - - -
156C ASP* 3.1 37.6 + - - +
208C ILE* 4.2 10.2 - - + +
209C PRO* 3.1 37.9 + - + +
211C ASP* 1.3 75.5 - - + +
213C ALA* 1.3 65.5 + - - +
214C LYS 3.3 0.2 + - - -
215C ARG* 3.3 11.6 + - - +
216C ILE* 3.2 36.8 + - + +
285C ARG* 3.9 18.4 - - - +
286C SER* 3.7 21.9 + - - +
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Residues in contact with ALA 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 4.4 8.2 - - + +
89C ILE* 3.8 35.0 - - + +
183C VAL* 4.0 18.8 - - + -
208C ILE* 4.1 4.8 - - + +
209C PRO 3.0 15.4 + - - +
210C VAL* 3.8 9.2 - - + +
212C GLN* 1.3 76.1 - - - +
214C LYS* 1.3 57.0 + - - +
216C ILE* 3.8 1.7 - - - +
217C ALA* 2.9 31.7 + - - +
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Residues in contact with LYS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 6.0 1.8 - - - -
105C LEU* 3.9 33.6 - - + +
210C VAL* 2.8 26.9 + - + +
211C ASP* 4.1 4.7 - - - +
213C ALA* 1.3 75.0 - - - +
215C ARG* 1.3 68.7 + - - +
217C ALA* 3.9 4.9 - - - +
218C ASP* 2.9 45.8 + - - +
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Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ASP 3.2 16.7 + - - +
212C GLN* 3.3 9.8 + - - +
214C LYS* 1.3 82.3 - - - +
216C ILE* 1.3 82.8 + - - +
218C ASP* 3.4 5.5 + - - +
219C GLU* 3.1 46.2 + - + +
227C SER 3.3 25.1 + - - -
228C HIS* 5.3 3.4 + - - +
229C ALA 5.5 0.2 - - - +
285C ARG* 4.0 13.3 + - - +
287C LYS 3.2 19.4 + - - -
288C ALA* 3.4 37.1 - - - +
289C PRO* 4.2 1.8 - - - +
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Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ASP* 4.0 4.5 - - + +
87C SER* 3.3 41.5 - - - +
89C ILE* 3.9 18.8 - - + -
208C ILE* 6.4 0.7 - - + -
212C GLN* 3.2 24.0 + - + +
213C ALA 4.0 2.2 - - - +
215C ARG* 1.3 98.0 - - - +
217C ALA* 1.3 59.5 + - - +
219C GLU* 3.3 6.9 + - - +
220C LEU* 2.9 36.4 + - + +
226C ALA* 3.8 23.1 - - + -
227C SER 5.4 1.1 - - - +
228C HIS* 5.3 4.5 - - - +
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Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.4 14.4 - - + -
45C LEU* 4.1 15.0 - - + -
89C ILE* 4.3 1.3 - - + +
91C VAL* 3.8 24.4 - - + +
213C ALA 2.9 24.1 + - - +
214C LYS* 3.9 5.8 - - - +
216C ILE* 1.3 72.8 - - - +
218C ASP* 1.3 58.8 + - - +
220C LEU* 3.4 3.1 + - - +
221C ILE* 2.9 36.9 + - + +
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Residues in contact with ASP 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LYS* 2.9 45.0 + - - +
215C ARG* 3.6 6.5 - - - +
217C ALA* 1.3 77.0 - - - +
219C GLU* 1.3 58.9 + - + +
221C ILE* 3.4 13.7 + - - +
222C SER* 3.0 31.6 + - - -
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Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ARG* 3.1 42.1 + - + +
216C ILE* 3.3 7.3 + - - +
218C ASP* 1.3 73.3 - - + +
220C LEU* 1.3 59.6 + - - +
222C SER* 4.1 5.4 - - - -
223C THR* 2.8 29.6 + - - +
224C GLY 3.3 4.3 + - - -
225C LYS 3.3 15.3 - - - +
226C ALA* 3.2 7.0 - - - +
227C SER* 2.8 42.5 + - - +
288C ALA* 5.5 0.5 - - - +
289C PRO* 5.4 1.0 - - - +
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Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C VAL* 3.9 10.7 - - - +
82C GLY* 3.8 28.3 - - - +
83C ALA 4.0 11.0 - - - +
84C ASP* 4.1 1.8 - - + +
89C ILE* 3.6 26.0 - - + +
90C ALA* 4.1 1.3 - - - -
91C VAL* 4.1 17.3 - - + -
216C ILE* 2.9 31.9 + - + +
217C ALA 3.7 3.8 - - - +
219C GLU* 1.3 74.7 - - - +
221C ILE* 1.3 60.2 + - - +
224C GLY* 3.0 45.0 + - - +
225C LYS* 3.9 0.4 - - - -
226C ALA* 3.8 22.7 - - + +
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Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.2 15.0 - - + -
43C LEU* 3.8 34.1 - - + -
81C VAL* 4.2 11.9 - - + +
91C VAL* 3.9 26.0 - - + -
93C ARG* 5.6 5.3 + - - +
217C ALA* 2.9 26.3 + - + +
218C ASP* 3.8 13.2 - - - +
219C GLU 3.3 0.2 - - - -
220C LEU* 1.3 79.4 - - - +
222C SER* 1.3 63.1 + - - +
224C GLY 4.9 0.2 + - - -
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Residues in contact with SER 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ASP 3.0 17.8 + - - -
219C GLU* 3.8 4.3 + - - -
221C ILE* 1.3 83.0 - - - +
223C THR* 1.3 70.0 + - - +
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Residues in contact with THR 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C GLU* 2.8 18.3 + - - +
222C SER* 1.3 80.8 + - - +
224C GLY* 1.3 58.1 + - - +
225C LYS* 3.1 22.9 + - + +
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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