Contacts of the helix formed by residues 264 - 279 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ARG* 5.0 4.6 - - - +
239B LYS* 4.5 10.3 - - - -
263B GLY* 1.3 75.0 - - - -
265B HIS* 1.3 67.4 + - - -
266B SER* 3.2 3.1 - - - -
267B LEU* 3.0 8.8 + - - +
268B ASN* 2.8 29.3 + - - +
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Residues in contact with HIS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.4 21.3 + - + +
58B HIS* 4.3 4.7 - - - -
59B SER* 3.8 23.1 - - - -
60B THR* 3.0 19.4 + - - +
78B GLU* 3.3 17.4 + - + -
239B LYS* 6.1 2.6 + - - -
242B ASP* 3.7 24.6 + - + -
246B ASP* 2.6 28.3 + - - -
264B GLY* 1.3 70.1 - - - -
266B SER* 1.3 57.7 + - - +
268B ASN* 3.3 1.5 + - - +
269B VAL* 2.9 35.2 + - - +
802B PAM 3.0 30.0 + - + +
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 2.9 35.5 + - - -
57B ASN* 3.6 10.2 + - - -
264B GLY 3.0 1.2 + - - -
265B HIS* 1.3 78.2 - - - +
267B LEU* 1.3 58.9 + - - +
269B VAL* 3.4 2.8 + - - +
270B LYS* 2.9 27.8 + - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 3.9 20.0 - - + +
139B GLU 4.1 4.3 - - - +
140B ASP* 3.9 26.5 - - + -
143B ARG* 3.8 18.6 - - + -
144B LEU* 3.7 26.7 - - - +
145B ILE* 3.4 31.0 - - + +
263B GLY* 4.2 5.4 - - - -
264B GLY* 3.0 12.3 + - - +
266B SER* 1.3 76.9 - - - +
268B ASN* 1.3 60.7 + - - +
270B LYS* 3.0 15.3 + - + +
271B LEU* 2.8 30.1 + - - +
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Residues in contact with ASN 268 (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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145B ILE* 3.1 24.0 - - - +
239B LYS 5.3 0.2 + - - -
242B ASP* 4.3 2.6 - - - +
243B LEU* 3.4 40.6 - - + +
246B ASP* 2.9 32.1 + - + +
247B LEU* 5.5 0.5 - - - +
260B SER* 4.7 0.3 + - - -
263B GLY* 4.4 2.3 - - - -
264B GLY* 2.8 27.1 + - - +
265B HIS* 3.4 9.2 + - - +
267B LEU* 1.3 74.8 - - - +
269B VAL* 1.3 57.6 + - - +
271B LEU* 3.2 6.4 + - - +
272B VAL* 2.9 31.8 + - - +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 5.2 2.2 - - + -
53B VAL* 4.4 18.2 - - + -
56B THR* 3.9 18.6 - - + -
60B THR* 4.5 9.4 - - + -
246B ASP* 4.7 5.8 - - + +
249B LEU* 4.3 21.3 - - + -
265B HIS 2.9 20.6 + - - +
266B SER 3.8 3.1 - - - +
268B ASN* 1.3 73.7 - - - +
270B LYS* 1.3 67.8 + - - +
272B VAL* 3.1 7.9 + - + +
273B LYS* 2.9 50.2 + - + +
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Residues in contact with LYS 270 (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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138B VAL* 4.8 7.9 - - + +
139B GLU 3.5 22.1 + - - +
140B ASP* 4.2 12.4 + - - +
266B SER 2.9 15.1 + - - +
267B LEU* 3.0 24.9 + - + +
269B VAL* 1.3 77.8 - - - +
271B LEU* 1.3 60.2 + - - +
273B LYS* 3.5 8.7 + - - +
274B GLU* 2.9 44.7 + - + +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 4.1 20.4 - - + -
138B VAL* 3.8 29.1 - - + +
145B ILE* 3.4 31.2 - - + +
147B ALA* 4.5 3.1 - - + -
243B LEU* 5.4 3.4 - - + -
247B LEU* 4.5 8.5 - - + -
258B PHE* 3.9 26.5 - - + -
267B LEU 2.8 12.5 + - - +
268B ASN* 3.3 9.0 - - - +
270B LYS* 1.3 74.7 - - - +
272B VAL* 1.3 68.3 + - - +
274B GLU* 3.0 6.8 + - - +
275B LEU* 2.9 39.5 + - + +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 3.7 28.3 - - + -
246B ASP* 3.6 22.9 - - + +
247B LEU* 4.1 22.9 - - + -
249B LEU* 4.3 3.8 - - + -
250B LEU* 3.5 34.9 - - + +
268B ASN 2.9 21.4 + - - +
269B VAL* 3.1 12.5 + - + +
271B LEU* 1.3 79.0 - - - +
273B LYS* 1.3 62.4 + - - +
275B LEU* 3.4 3.0 + - - +
276B ALA* 3.0 20.1 + - - +
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Residues in contact with LYS 273 (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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50B HIS* 3.2 46.0 + - + +
51B GLU* 4.5 4.4 + - - +
53B VAL* 5.2 5.1 + - - +
269B VAL* 2.9 41.6 + - + +
270B LYS* 3.8 7.0 - - - +
272B VAL* 1.3 71.9 - - - +
274B GLU* 1.3 67.2 + - - +
276B ALA* 3.8 6.1 - - - +
277B LYS* 2.9 26.8 + - - +
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.4 19.5 - - + -
137B ILE 5.1 0.9 - - - +
138B VAL* 3.5 26.1 - - + +
270B LYS* 2.9 36.0 + - + +
271B LEU 3.0 7.0 + - - +
273B LYS* 1.3 78.0 - - - +
275B LEU* 1.3 64.2 + - - +
277B LYS* 3.1 14.1 + - - +
278B LYS* 2.9 28.8 + - + +
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Residues in contact with LEU 275 (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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130B PHE* 3.8 15.0 - - + -
132B VAL* 4.2 19.5 - - + -
134B GLU 5.3 0.7 - - - +
136B ILE* 3.9 25.3 - - + +
147B ALA* 4.8 0.2 - - + -
247B LEU* 5.0 0.9 - - + -
250B LEU* 4.1 21.1 - - + -
258B PHE* 4.2 17.9 - - + -
271B LEU* 2.9 35.1 + - + +
272B VAL* 3.6 7.2 - - - +
274B GLU* 1.3 79.2 - - - +
276B ALA* 1.3 63.0 + - - +
278B LYS* 3.3 10.4 + - + +
279B GLN* 3.1 42.2 + - - +
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Residues in contact with ALA 276 (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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50B HIS* 3.5 33.4 - - + +
130B PHE* 4.3 12.3 - - + -
250B LEU* 4.2 7.3 - - + +
272B VAL 3.0 16.3 + - - +
273B LYS 3.8 3.4 - - - +
275B LEU* 1.3 76.0 - - - +
277B LYS* 1.3 66.4 + - - +
279B GLN 3.2 20.1 + - - +
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Residues in contact with LYS 277 (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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273B LYS 2.9 19.5 + - - +
274B GLU* 3.3 15.7 - - - +
276B ALA* 1.3 78.9 - - - +
278B LYS* 1.3 65.8 + - + +
279B GLN 3.3 2.9 + - - -
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Residues in contact with LYS 278 (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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134B GLU* 2.9 52.3 + - - +
135B PRO 3.4 10.7 + - - -
136B ILE* 3.8 32.7 - - + +
274B GLU* 2.9 14.7 + - + +
275B LEU* 3.7 12.9 - - + +
277B LYS* 1.3 78.8 - - + +
279B GLN* 1.3 67.2 + - + +
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Residues in contact with GLN 279 (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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130B PHE* 3.3 40.9 - - + -
131B VAL 2.9 26.0 + - - +
132B VAL* 4.0 2.4 - - - +
133B GLU* 3.5 38.3 - - + +
134B GLU 5.6 0.2 - - - +
275B LEU* 3.1 22.0 + - - +
276B ALA* 3.2 14.5 + - - +
277B LYS 4.1 3.4 - - - -
278B LYS* 1.3 88.9 - - + +
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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