Contacts of the helix formed by residues 248 - 260 (chain B) in PDB entry 3GYQ
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 ASN 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ALA* 4.2 23.5 - - + +
135A ARG* 3.9 25.6 - - + +
136A THR* 5.4 3.6 + - - +
129B ASN* 4.1 18.2 + - - +
247B LEU* 1.3 72.9 - - - +
249B VAL* 1.3 79.3 + - - +
250B SER* 2.8 27.5 + - - -
251B VAL* 2.9 21.3 + - + +
252B SER* 2.8 25.8 + - - -
270B SAM 5.1 1.3 - - - -
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 4.6 0.4 - - + -
124B VAL* 4.4 12.3 - - + -
129B ASN* 4.0 27.1 - - + +
133B ILE* 3.9 16.6 - - + -
217B PHE* 3.8 22.7 - - + -
218B GLY 3.6 19.3 - - - +
219B SER* 5.6 2.0 - - - -
247B LEU 3.5 2.4 + - - -
248B ASN* 1.3 82.3 + - - +
250B SER* 1.3 58.4 + - - +
252B SER* 3.3 2.5 + - - -
253B LEU* 2.9 27.1 + - + +
270B SAM 3.6 27.9 - - + +
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Residues in contact with SER 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A SER* 4.8 4.2 + - - -
251A VAL* 3.8 18.8 - - - +
129B ASN* 4.5 8.7 + - - -
132B ALA* 4.4 19.2 - - - +
133B ILE* 3.8 25.4 - - - -
136B THR* 4.9 1.6 + - - -
248B ASN* 2.8 23.8 + - - -
249B VAL* 1.3 81.0 - - - +
251B VAL* 1.3 66.4 + - - +
253B LEU* 3.4 4.5 + - - +
254B GLY* 3.1 16.3 + - - -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 5.4 2.2 - - + +
136A THR* 3.8 25.4 - - + +
250A SER* 4.0 31.6 - - - +
251A VAL* 4.5 8.5 - - + +
254A GLY* 4.1 22.0 - - - -
255A ILE* 5.8 0.2 - - - +
247B LEU* 4.1 20.2 - - + -
248B ASN* 2.9 24.5 + - + +
250B SER* 1.3 81.5 + - - +
252B SER* 1.3 66.1 + - - +
254B GLY* 3.2 2.3 + - - -
255B ILE* 3.2 24.2 + - + +
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B PHE* 3.8 9.2 - - - -
238B ILE* 3.6 18.1 - - - +
247B LEU* 3.2 14.2 - - - +
248B ASN 2.8 12.4 + - - -
249B VAL 3.6 7.6 - - - -
251B VAL* 1.3 73.2 - - - +
253B LEU* 1.3 62.2 + - - +
255B ILE 3.5 0.5 + - - -
256B ALA* 3.1 23.7 + - - +
270B SAM 3.1 49.7 + - - -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.6 28.5 - - + -
121B LEU* 5.5 0.4 - - + -
133B ILE* 3.3 45.5 - - + +
136B THR* 4.2 12.3 - - - -
137B SER* 3.5 11.4 - - - +
217B PHE* 3.4 34.9 - - + -
249B VAL 2.9 17.4 + - - +
250B SER* 3.5 5.4 - - - +
251B VAL 3.2 0.2 - - - -
252B SER* 1.3 74.9 - - - +
254B GLY* 1.3 64.6 + - - +
256B ALA* 3.3 1.4 + - - +
257B LEU* 3.0 35.9 + - + +
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Residues in contact with GLY 254 (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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251A VAL* 4.1 12.1 - - - -
255A ILE* 3.8 7.0 - - - +
136B THR* 3.8 22.4 - - - +
140B LEU* 3.4 6.7 - - - +
250B SER 3.1 10.4 + - - -
251B VAL 3.2 4.2 + - - -
253B LEU* 1.3 79.4 - - - +
255B ILE* 1.3 56.7 + - - +
258B HIS* 2.9 30.0 + - - +
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Residues in contact with ILE 255 (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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140A LEU* 4.7 3.6 - - + -
254A GLY* 3.8 32.3 - - - +
255A ILE* 4.3 4.9 - - + +
258A HIS* 3.5 43.1 - - + +
203B VAL* 4.5 5.8 - - + -
238B ILE* 3.9 27.6 - - + -
247B LEU* 4.0 18.6 - - + -
251B VAL* 3.2 14.6 + - + +
252B SER 3.9 5.4 - - - +
254B GLY* 1.3 73.7 - - - +
256B ALA* 1.3 65.8 + - - +
258B HIS* 3.1 8.2 + - - +
259B GLU* 3.0 22.5 + - - +
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Residues in contact with ALA 256 (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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195B LEU* 3.4 33.9 - - + -
203B VAL* 3.9 13.9 - - + +
206B LEU* 4.1 4.0 - - + +
215B LEU* 4.3 11.4 - - + -
217B PHE* 4.0 8.7 - - + -
238B ILE* 4.9 0.2 - - - +
252B SER 3.1 12.1 + - - +
253B LEU 3.3 3.8 + - - +
255B ILE* 1.3 76.9 - - - +
257B LEU* 1.3 62.5 + - - +
259B GLU* 3.2 12.8 + - - +
260B ARG* 3.3 18.6 + - - +
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Residues in contact with LEU 257 (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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117B ASP* 4.8 4.5 - - + +
119B VAL* 4.2 10.8 - - + -
136B THR* 4.1 9.0 - - + +
137B SER* 3.7 31.9 - - - +
140B LEU* 3.6 24.8 - - + +
142B ALA* 4.4 10.5 - - + +
215B LEU* 3.7 24.0 - - + -
253B LEU* 3.0 39.9 + - + +
256B ALA* 1.3 74.6 - - - +
258B HIS* 1.3 65.8 + - - +
260B ARG* 3.1 5.5 + - - +
261B ILE* 3.0 22.3 + - - +
264B ASN* 4.4 16.1 - - - +
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Residues in contact with HIS 258 (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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203A VAL* 3.7 25.8 - - + -
204A LYS* 3.9 13.7 + - + +
238A ILE* 4.3 11.4 - - + +
239A PRO* 4.7 10.2 + - + +
255A ILE* 3.7 28.6 - - + +
258A HIS* 4.4 7.4 - + - -
259A GLU* 2.9 30.9 + - - -
140B LEU* 3.8 7.9 - - + +
254B GLY 2.9 19.8 + - - +
255B ILE* 3.1 7.1 + - - +
257B LEU* 1.3 77.1 - - - +
259B GLU* 1.3 69.9 + - - +
261B ILE* 3.3 30.8 - - + +
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Residues in contact with GLU 259 (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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204A LYS* 3.5 17.7 + - - +
258A HIS* 2.7 31.0 + - - +
259A GLU* 3.8 0.7 - - - +
203B VAL* 3.6 32.1 - - + +
204B LYS* 2.9 38.0 + - - +
206B LEU* 4.4 5.4 - - + -
207B GLY* 3.6 22.6 + - - +
255B ILE 3.0 13.7 + - - +
256B ALA 3.2 7.6 + - - +
258B HIS* 1.3 77.1 - - - +
260B ARG* 1.3 60.0 + - - +
261B ILE* 3.4 1.0 + - - +
262B ASP* 5.0 2.4 + - - +
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Residues in contact with ARG 260 (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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117B ASP* 2.7 41.5 + - - +
206B LEU* 2.9 44.4 + - + -
207B GLY 4.5 0.2 - - - +
209B ASN* 2.7 34.1 + - - +
210B PRO 5.2 0.2 - - - -
211B ASP 3.0 23.0 + - - -
212B ARG* 4.6 0.4 - - - +
213B LEU* 3.5 13.1 - - + +
215B LEU* 4.7 6.7 - - + -
256B ALA 3.3 13.7 + - - +
257B LEU* 3.1 12.1 + - + +
259B GLU* 1.3 78.4 - - - +
261B ILE* 1.3 65.5 + - - +
262B ASP 3.2 2.7 - - - -
263B ARG* 3.0 30.5 + - - +
264B ASN* 2.9 28.4 + - - +
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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