Contacts of the helix formed by residues 213 - 219 (chain B) in PDB entry 1YI2
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17330 A 3.1 31.8 + - - -
17340 C 3.8 5.3 + - - -
212B GLN* 1.3 76.4 + - - +
214B PRO* 1.3 66.3 - - - +
215B VAL 3.3 2.9 - - - -
216B LYS* 3.2 4.9 + - - +
217B ARG* 2.7 36.1 + - - +
234B ARG* 5.4 0.2 - - - -
254B GLN* 4.5 0.9 - - - -
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Residues in contact with PRO 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17330 A 4.9 0.9 - - - +
17340 C 4.8 3.4 - - - +
213B GLY* 1.3 81.7 - - - +
215B VAL* 1.3 61.1 + - - +
218B TRP* 2.7 41.5 + - + +
219B GLY 3.1 5.4 + - - -
220B VAL* 3.5 20.7 + - + -
234B ARG 4.2 17.5 - - - +
235B ARG* 5.5 0.9 - - - -
236B ILE* 4.1 17.9 - - + +
252B PRO 4.0 16.2 - - - +
253B GLN* 4.2 0.7 - - - -
254B GLN* 4.0 22.6 - - + +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20380 A 4.3 9.2 - - - +
20390 A 3.8 8.3 - - - +
213B GLY 3.3 0.6 - - - -
214B PRO* 1.3 76.9 - - - +
216B LYS* 1.3 58.2 + - - +
219B GLY* 2.9 26.3 + - - -
220B VAL* 3.4 19.3 - - + +
221B GLN 3.5 24.2 - - - +
222B LYS* 4.3 13.0 - - + -
234B ARG* 3.6 62.4 - - + +
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20390 A 4.8 10.3 - - - +
20400 C 5.0 6.9 + - - +
27590 C 4.6 1.5 + - - -
27600 C 3.1 39.3 + - - -
209B LYS* 3.7 25.5 - - - +
212B GLN* 3.1 39.3 - - + +
213B GLY 3.2 7.9 + - - +
215B VAL* 1.3 81.0 - - - +
217B ARG* 1.3 64.6 + - - +
219B GLY* 4.3 2.1 + - - -
234B ARG* 4.7 5.5 - - - +
257B THR* 5.0 1.3 - - - +
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Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26550 U 3.0 20.4 + - - -
26560 G 3.0 16.4 + - - -
27150 G 5.2 1.9 + - - -
16B ARG* 2.8 52.7 + - + +
212B GLN 4.0 1.1 - - - -
213B GLY 2.7 22.8 + - - +
216B LYS* 1.3 74.6 - - - +
218B TRP* 1.3 81.7 + - + +
253B GLN 2.8 28.3 + - - -
254B GLN 3.3 1.0 + - - -
255B GLY* 3.4 14.8 - - - +
256B GLN 2.8 25.0 + - - +
257B THR* 3.2 29.9 - - + +
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Residues in contact with TRP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26550 U 5.2 1.8 - - - -
26560 G 4.7 8.5 - - - -
27140 U 5.0 0.3 + - - -
27150 G 5.8 0.9 - - - -
7B ARG* 5.3 1.6 - - - -
8B LYS* 3.4 40.8 - - - +
9B GLY* 3.4 12.4 + - - -
10B SER 3.4 23.3 - - - -
11B LEU* 4.5 15.5 - - + -
16B ARG* 3.7 33.0 - - - -
214B PRO* 2.7 19.8 + - + +
217B ARG* 1.3 104.7 - - + +
219B GLY* 1.3 62.6 + - - +
220B VAL* 4.1 2.2 - - + -
250B THR 6.2 0.2 - - - -
251B VAL 5.6 2.0 - - - -
252B PRO* 3.6 34.8 - - + -
253B GLN 3.1 31.3 + - - +
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Residues in contact with GLY 219 (chain B).
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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8B LYS* 3.7 15.2 + - - +
215B VAL 2.9 18.4 + - - -
216B LYS 4.3 2.4 + - - -
217B ARG 3.8 0.6 - - - -
218B TRP* 1.3 79.3 - - - +
220B VAL* 1.3 64.5 + - - +
221B GLN* 4.0 0.3 + - - +
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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