Contacts of the helix formed by residues 264 - 279 (chain A) in PDB entry 1YH8
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 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG* 5.0 5.0 - - - +
239A LYS* 4.5 10.8 - - - -
263A GLY* 1.3 74.3 - - - -
265A HIS* 1.3 67.4 + - - -
266A SER* 3.1 3.6 - - - -
267A LEU* 3.0 8.0 + - - +
268A ASN* 2.8 28.5 + - - +
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Residues in contact with HIS 265 (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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56A THR* 3.3 21.3 + - - +
58A HIS* 4.3 5.2 - - - -
59A SER* 3.7 23.3 - - - -
60A THR* 3.0 19.0 + - - +
78A GLU* 3.3 20.7 + - + -
239A LYS* 6.1 2.4 + - - -
242A ASP* 3.7 24.6 + - + -
246A ASP* 2.6 30.0 + - - -
264A GLY* 1.3 70.3 - - - -
266A SER* 1.3 56.4 + - - +
268A ASN* 3.3 1.3 + - - +
269A VAL* 2.9 35.9 + - - +
801A PAM 3.0 25.7 + - + -
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 2.9 35.5 + - - -
57A ASN* 3.6 9.7 + - - -
264A GLY 3.0 1.5 + - - -
265A HIS* 1.3 77.7 - - - +
267A LEU* 1.3 58.8 + - - +
269A VAL* 3.4 2.3 + - - +
270A LYS* 2.9 27.8 + - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.0 20.1 - - + +
139A GLU 4.1 4.3 - - - +
140A ASP* 3.9 25.8 - - + -
143A ARG* 3.8 18.2 - - + -
144A LEU* 3.7 26.7 - - - +
145A ILE* 3.4 30.7 - - + +
263A GLY* 4.2 4.9 - - - -
264A GLY 3.0 12.3 + - - +
266A SER* 1.3 75.6 - - - +
268A ASN* 1.3 67.9 + - - +
270A LYS* 3.0 16.2 + - + +
271A LEU* 2.8 23.6 + - - +
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Residues in contact with ASN 268 (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 ILE* 3.1 23.1 - - - +
239A LYS 5.3 0.4 + - - -
242A ASP* 4.4 2.4 - - - +
243A LEU* 3.5 39.3 - - + +
246A ASP* 2.9 32.7 + - + +
247A LEU* 5.5 0.3 - - - +
260A SER* 4.7 0.5 + - - -
263A GLY* 4.4 1.8 - - - -
264A GLY* 2.8 28.2 + - - +
265A HIS* 3.4 9.2 + - - +
267A LEU* 1.3 76.0 - - - +
269A VAL* 1.3 57.0 + - - +
271A LEU* 3.2 6.6 + - - +
272A VAL* 2.9 32.4 + - + +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A HIS* 5.2 2.0 - - + -
53A VAL* 4.4 19.7 - - + -
56A THR* 3.9 18.6 - - + -
60A THR* 4.5 7.2 - - + -
246A ASP* 4.8 5.6 - - + +
249A LEU* 4.4 21.3 - - + -
265A HIS 2.9 21.2 + - - +
266A SER 3.8 4.0 - - - +
268A ASN* 1.3 72.2 - - - +
270A LYS* 1.3 67.4 + - - +
272A VAL* 3.1 8.5 + - + +
273A LYS* 2.9 51.5 + - + +
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Residues in contact with LYS 270 (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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138A VAL* 4.8 7.9 - - + -
139A GLU 3.5 20.4 + - - +
140A ASP* 4.2 12.3 + - - +
266A SER 2.9 16.2 + - - +
267A LEU* 3.0 24.9 + - + +
269A VAL* 1.3 77.2 - - - +
271A LEU* 1.3 59.5 + - - +
273A LYS* 3.5 8.9 + - - +
274A GLU* 2.9 44.2 + - + +
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Residues in contact with LEU 271 (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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136A ILE* 4.1 20.4 - - + +
138A VAL* 3.8 26.6 - - + +
145A ILE* 3.4 30.5 - - + +
147A ALA* 4.6 2.9 - - + -
243A LEU* 5.4 3.4 - - + -
247A LEU* 4.5 8.5 - - + -
258A PHE* 3.9 26.9 - - + -
267A LEU 2.8 11.0 + - - +
268A ASN* 3.3 9.9 - - - +
269A VAL 3.1 0.2 - - - -
270A LYS* 1.3 75.6 - - - +
272A VAL* 1.3 68.2 + - - +
274A GLU* 3.0 8.5 + - - +
275A LEU* 2.9 40.2 + - + +
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Residues in contact with VAL 272 (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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50A HIS* 3.7 29.2 - - + -
246A ASP* 3.6 22.2 - - + +
247A LEU* 4.1 21.5 - - + -
249A LEU* 4.3 4.5 - - + -
250A LEU* 3.5 34.0 - - + +
268A ASN 2.9 21.2 + - - +
269A VAL* 3.4 11.4 - - - +
271A LEU* 1.3 79.2 - - - +
273A LYS* 1.3 63.2 + - - +
275A LEU* 3.4 2.9 + - - +
276A ALA* 3.0 20.4 + - - +
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Residues in contact with LYS 273 (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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50A HIS* 3.2 43.4 + - + +
51A GLU* 4.5 4.8 - - - +
53A VAL* 5.2 6.0 + - - +
269A VAL* 2.9 40.3 + - + +
270A LYS* 3.8 7.9 - - - +
272A VAL* 1.3 74.1 - - - +
274A GLU* 1.3 65.7 + - - +
276A ALA* 3.4 5.4 + - - +
277A LYS* 2.9 27.8 + - - +
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Residues in contact with GLU 274 (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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136A ILE* 3.4 20.6 - - + +
137A ILE 5.1 0.9 - - - +
138A VAL* 3.5 26.6 - - + +
270A LYS* 2.9 36.0 + - + +
271A LEU 3.0 6.1 + - - +
273A LYS* 1.3 77.3 - - - +
275A LEU* 1.3 65.2 + - - +
277A LYS* 3.1 13.7 + - - +
278A LYS* 2.9 30.0 + - + +
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Residues in contact with LEU 275 (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 PHE* 3.8 14.4 - - + -
132A VAL* 4.2 18.4 - - + -
134A GLU 5.3 0.9 - - - +
136A ILE* 3.9 24.2 - - + +
147A ALA* 4.8 0.4 - - + -
247A LEU* 4.9 0.4 - - + -
250A LEU* 4.1 21.3 - - + -
258A PHE* 4.1 18.2 - - + -
271A LEU* 2.9 35.2 + - + +
272A VAL* 3.6 6.7 - - - +
274A GLU* 1.3 80.3 - - - +
276A ALA* 1.3 62.9 + - - +
278A LYS* 3.3 10.9 + - + +
279A GLN* 3.1 42.2 + - - +
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Residues in contact with ALA 276 (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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50A HIS* 3.5 33.0 - - + +
130A PHE* 4.3 11.4 - - + -
250A LEU* 4.2 8.6 - - + +
272A VAL 3.0 16.3 + - - +
273A LYS 3.8 3.1 - - - +
275A LEU* 1.3 75.3 - - - +
277A LYS* 1.3 66.3 + - - +
279A GLN 3.2 20.8 + - - +
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Residues in contact with LYS 277 (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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273A LYS 2.9 18.5 + - - +
274A GLU* 3.3 15.9 - - - +
276A ALA* 1.3 78.5 - - - +
278A LYS* 1.3 65.6 + - + +
279A GLN 4.1 3.5 - - - -
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Residues in contact with LYS 278 (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 GLU* 2.9 52.7 + - - +
135A PRO 3.4 11.1 + - - -
136A ILE* 3.8 31.6 - - + +
274A GLU* 2.9 15.2 + - + +
275A LEU* 3.7 12.3 - - + +
277A LYS* 1.3 78.9 - - + +
279A GLN* 1.3 67.0 + - + +
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Residues in contact with GLN 279 (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 PHE* 3.2 41.1 - - + -
131A VAL 2.9 25.1 + - - +
132A VAL* 4.0 2.8 - - - +
133A GLU* 3.5 39.0 - - + +
275A LEU* 3.1 22.2 + - - +
276A ALA* 3.2 14.0 + - - +
277A LYS 4.1 2.7 - - - -
278A LYS* 1.3 88.2 - - + +
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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