Contacts of the helix formed by residues 213 - 225 (chain A) in PDB entry 5HNK
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 GLY 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A LEU* 4.0 2.3 - - - +
199A MET* 3.7 17.0 - - - +
212A ILE* 1.3 73.7 - - - +
214A ALA* 1.3 59.9 + - - -
217A GLY* 3.0 27.4 + - - -
9Y A 2.9 38.7 + - - -
10Y C 4.4 1.1 - - - -
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Residues in contact with ALA 214 (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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184A HIS 5.7 0.9 - - - +
185A ASN* 5.0 21.1 - - + +
195A LEU* 4.1 14.0 - - + +
199A MET* 3.6 21.7 - - + +
213A GLY* 1.3 71.2 - - - -
215A LYS* 1.3 61.7 + - + +
218A TYR* 3.0 30.7 + - - +
9Y A 3.5 5.4 + - - +
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Residues in contact with LYS 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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181A TYR* 4.5 5.4 + - - +
185A ASN* 4.9 18.4 - - + +
214A ALA* 1.3 77.7 - - + +
216A ARG* 1.3 65.6 + - + +
218A TYR* 3.3 8.6 + - + +
219A ASN* 3.1 33.1 + - - +
182B GLU 4.1 7.9 + - - -
183B HIS* 3.1 33.7 + - - +
185B ASN* 5.2 2.2 - - - +
8Y T 3.7 47.7 + - - +
9Y A 3.1 16.4 + - - +
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Residues in contact with ARG 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 GLY* 2.9 31.4 + - - -
212A ILE* 4.2 9.0 - - + -
215A LYS* 1.3 75.0 - - + +
217A GLY* 1.3 58.3 + - - +
219A ASN* 3.3 10.8 + - - +
220A ILE* 3.0 36.8 + - - +
242A TYR* 3.3 53.1 - - + +
170B THR 5.6 3.8 + - - -
11X G 5.8 3.0 + - - -
12X C 6.4 0.6 - - - -
7Y G 5.9 2.4 - - - +
8Y T 4.0 20.4 + - - +
9Y A 2.9 29.0 + - - +
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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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195A LEU* 3.7 16.6 - - - -
198A ILE* 4.7 4.7 - - - +
212A ILE* 3.5 14.4 - - - +
213A GLY 3.0 20.2 + - - -
216A ARG* 1.3 77.2 - - - +
218A TYR* 1.3 56.2 + - - +
220A ILE* 3.5 4.8 + - - +
221A ILE* 3.1 34.8 + - - +
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Residues in contact with TYR 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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181A TYR* 3.5 31.8 - + - -
185A ASN* 3.6 18.6 - - + +
186A VAL* 4.1 8.5 - - + -
187A ASP* 2.9 26.2 + - - -
191A GLN* 3.5 25.8 - - - -
195A LEU* 4.0 2.5 - - - +
214A ALA 3.0 19.7 + - - +
215A LYS* 3.6 9.0 - - + +
217A GLY* 1.3 76.8 - - - +
219A ASN* 1.3 67.5 + - - +
221A ILE* 3.3 7.6 + - + +
222A ARG* 2.9 51.0 + - + +
173B ARG* 5.6 4.3 - - - -
182B GLU* 3.8 20.3 - - + +
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Residues in contact with ASN 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 LYS* 3.1 23.4 + - - +
216A ARG* 3.3 12.2 + - - +
218A TYR* 1.3 86.1 - - - +
220A ILE* 1.3 58.0 + - + +
222A ARG* 3.8 5.5 - - - +
223A GLU* 3.0 35.5 + - - +
171B THR* 4.8 7.3 + - - -
173B ARG* 3.3 48.4 + - - +
8Y T 5.6 2.6 + - - -
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Residues in contact with ILE 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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198A ILE* 5.3 4.7 - - + -
212A ILE* 4.1 23.8 - - + -
216A ARG 3.0 27.5 + - - +
217A GLY* 3.8 4.3 - - - +
219A ASN* 1.3 75.7 - - + +
221A ILE* 1.3 57.8 + - + +
223A GLU* 4.6 1.8 - - - +
224A PHE* 2.8 51.4 + - + +
230A ILE* 3.8 22.7 - - + -
236A LEU* 4.3 1.8 - - + -
242A TYR* 4.0 22.7 - - + +
243A ILE* 4.6 9.9 - - + -
246A LEU* 4.3 20.6 - - + -
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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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186A VAL* 5.5 1.6 - - + -
191A GLN* 3.7 43.9 + - + +
194A SER* 3.9 6.7 - - - -
195A LEU* 3.7 37.0 - - + +
198A ILE* 4.0 16.8 - - + -
217A GLY 3.1 21.2 + - - +
218A TYR* 3.8 6.7 - - - +
220A ILE* 1.3 76.0 - - - +
222A ARG* 1.3 54.9 + - - +
225A GLY* 2.7 48.1 + - - +
226A ASN* 4.1 11.2 - - - +
230A ILE* 4.3 3.8 - - + -
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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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187A ASP* 3.5 25.2 + - - -
191A GLN* 3.9 12.0 - - - +
218A TYR* 2.9 46.1 + - + +
219A ASN* 3.8 6.1 - - - +
221A ILE* 1.3 76.5 - - - +
223A GLU* 1.3 61.6 + - - +
225A GLY 4.5 1.2 + - - -
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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 ASN* 3.0 20.7 + - - +
220A ILE* 5.3 0.3 - - - -
222A ARG* 1.3 79.0 - - - +
224A PHE* 1.3 95.7 + - + +
172B ARG* 5.5 5.5 + - - -
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Residues in contact with PHE 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 ILE* 2.8 30.0 + - + +
223A GLU* 1.3 111.2 - - + +
225A GLY* 1.3 59.2 + - - +
229A ASP* 3.7 8.0 - - - +
230A ILE* 4.1 13.2 - - + -
233A GLN* 3.0 44.3 + - - +
236A LEU* 3.8 37.7 - - + -
237A PRO* 4.2 27.8 - - + -
243A ILE* 6.0 3.1 - - + -
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Residues in contact with GLY 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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221A ILE* 2.7 34.7 + - - +
222A ARG 4.5 1.2 + - - -
223A GLU 3.7 1.0 - - - -
224A PHE* 1.3 71.4 - - - +
226A ASN* 1.3 67.6 + - - +
229A ASP* 4.3 6.3 - - - -
230A ILE* 3.3 17.5 - - - +
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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