Contacts of the helix formed by residues 214 - 225 (chain A) in PDB entry 4KYI
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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155A LYS* 4.0 4.2 + - - +
210A ASN* 3.8 16.8 - - + +
212A ARG 3.2 15.2 + - - +
213A LEU* 1.3 74.2 - - - +
215A LEU* 1.3 64.0 + - - +
216A GLY* 3.4 2.1 + - - -
217A ASP* 2.3 43.7 + - - +
218A LEU 3.8 1.0 + - - -
220A ARG* 4.8 0.9 + - - -
257A PRO 3.0 18.3 + - - +
258A GLN* 3.7 28.9 + - - +
259A GLN 3.3 12.8 - - - -
260A SER* 3.8 2.0 - - - +
261A ILE* 3.3 20.7 - - - +
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Residues in contact with LEU 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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214A THR* 1.3 72.5 - - - +
216A GLY* 1.3 61.3 + - - +
218A LEU* 3.2 23.3 - - + +
236A LEU* 4.0 34.3 - - + +
238A VAL* 5.9 1.1 - - + -
251A TYR* 4.5 9.6 - - + +
252A SER 4.1 13.5 - - - +
253A GLU* 3.7 24.2 - - + +
256A THR* 3.7 25.4 - - - +
257A PRO 3.8 0.2 + - - -
259A GLN* 2.8 33.6 + - + +
260A SER 4.4 0.2 - - - +
261A ILE* 3.8 22.9 - - + -
264A VAL* 4.1 19.5 - - + -
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Residues in contact with GLY 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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214A THR* 3.2 0.9 - - - -
215A LEU* 1.3 75.7 - - - +
217A ASP* 1.3 60.3 + - - +
218A LEU 3.1 2.2 - - - -
219A GLY* 3.0 5.7 + - - -
220A ARG* 3.0 34.3 + - - +
253A GLU* 4.7 5.2 - - - -
257A PRO* 2.9 34.4 + - - -
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Residues in contact with ASP 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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130A MET* 3.7 15.6 - - + +
152A LEU* 3.3 23.3 - - + +
155A LYS* 2.9 40.3 + - - +
213A LEU* 3.7 4.5 - - + +
214A THR* 2.3 43.5 + - - +
215A LEU 3.2 0.2 - - - -
216A GLY* 1.3 74.8 - - - +
218A LEU* 1.3 61.6 + - - +
219A GLY 3.2 0.2 - - - -
220A ARG* 3.6 21.0 + - - +
221A LEU* 3.0 29.5 + - - +
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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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80A SER 5.8 0.7 - - - +
83A ALA* 3.7 24.2 - - + +
84A VAL* 4.8 10.5 - - + -
130A MET* 4.1 19.3 - - + -
214A THR 3.8 0.8 + - - -
215A LEU* 3.2 18.3 + - + +
216A GLY 3.1 0.2 - - - -
217A ASP* 1.3 80.5 - - - +
219A GLY* 1.3 57.4 + - - +
221A LEU* 3.9 1.8 - - - +
222A ARG* 3.3 12.8 + - - +
233A ILE* 3.2 37.1 - - + +
234A LYS 3.6 19.3 - - - +
236A LEU* 3.8 21.1 - - + +
253A GLU* 4.1 7.0 - - + +
261A ILE* 3.7 26.5 - - + -
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Residues in contact with GLY 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 LEU 3.8 1.6 + - - -
216A GLY 3.0 10.3 + - - -
218A LEU* 1.3 78.4 - - - +
220A ARG* 1.3 62.8 + - - +
222A ARG* 3.5 8.5 + - - +
223A GLU* 3.2 34.5 + - - +
253A GLU* 3.7 22.7 - - - -
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Residues in contact with ARG 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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147A MET* 5.7 3.2 - - - +
148A ASN* 3.9 36.6 + - + +
151A ILE* 3.5 31.5 - - - +
152A LEU* 4.1 24.7 - - + -
209A GLU* 3.0 32.0 + - - +
214A THR* 4.8 1.2 + - - -
216A GLY* 3.0 19.0 + - - +
217A ASP* 3.6 27.9 + - - +
219A GLY* 1.3 75.9 - - - +
221A LEU* 1.3 64.6 + - - +
222A ARG 3.4 0.2 + - - -
223A GLU* 3.4 3.8 + - - +
224A LEU* 3.3 28.2 + - - +
257A PRO 5.8 0.2 + - - -
258A GLN* 4.9 1.0 - - - +
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Residues in contact with LEU 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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130A MET* 3.8 39.0 - - + +
133A HIS* 3.7 37.5 - - + +
134A LEU* 4.4 11.4 - - + +
152A LEU* 3.7 17.6 - - + +
217A ASP 3.0 16.7 + - - +
218A LEU* 3.9 6.3 - - + +
220A ARG* 1.3 75.4 - - - +
222A ARG* 1.3 63.6 + - - +
224A LEU* 3.1 13.6 + - + +
225A LEU* 3.1 28.0 + - + +
233A ILE* 4.1 18.2 - - + -
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Residues in contact with ARG 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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67A THR 4.6 2.0 + - - -
218A LEU 3.3 12.7 + - - +
219A GLY* 3.9 9.3 + - - +
220A ARG 3.3 0.8 - - - -
221A LEU* 1.3 77.3 - - - +
223A GLU* 1.3 65.1 + - + +
224A LEU 3.3 0.3 + - - -
225A LEU* 3.4 9.1 + - - +
230A LYS* 3.3 56.4 - - + +
233A ILE* 2.6 60.6 + - + +
234A LYS* 3.3 17.8 + - - +
235A ASN* 3.5 6.8 - - - +
253A GLU* 2.4 38.3 + - - -
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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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145A GLN* 3.2 29.1 + - - +
148A ASN* 3.5 20.3 + - - +
219A GLY 3.2 20.7 + - - +
220A ARG* 3.8 4.8 - - - +
221A LEU 3.3 0.4 - - - -
222A ARG* 1.3 77.7 - - + +
224A LEU* 1.3 61.4 + - - +
225A LEU 3.7 4.0 - - - +
230A LYS* 3.8 19.3 + - - +
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Residues in contact with LEU 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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134A LEU* 3.6 28.3 - - + -
137A VAL* 4.0 27.3 - - + +
141A ILE* 5.6 2.7 - - + -
145A GLN* 3.4 31.5 - - + +
148A ASN* 3.6 20.2 - - + -
149A TYR* 3.8 32.8 - - + +
152A LEU* 4.4 7.4 - - + -
220A ARG 3.3 16.2 - - - +
221A LEU 3.1 9.5 + - - +
223A GLU* 1.3 77.9 - - - +
225A LEU* 1.3 66.4 + - - +
226A PRO* 3.6 1.9 - - - +
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Residues in contact with LEU 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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133A HIS* 3.5 35.0 - - + +
136A SER* 3.7 12.1 - - - +
137A VAL* 4.0 10.5 - - + +
221A LEU* 3.1 21.6 + - + +
222A ARG* 3.4 8.7 + - - +
223A GLU 3.7 0.7 - - - +
224A LEU* 1.3 81.7 - - - +
226A PRO* 1.3 78.4 - - + +
229A ASN* 3.6 28.3 - - + +
230A LYS* 3.2 22.8 - - + -
232A LEU* 4.6 9.2 - - + -
233A ILE* 4.1 25.1 - - + -
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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