Contacts of the helix formed by residues 253 - 267 (chain B) in PDB entry 1GQT
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 ALA 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B THR* 3.3 13.4 + - - +
251B ILE 3.2 4.0 + - - -
252B ALA* 1.3 77.1 - - - +
254B GLY* 1.3 58.3 + - - +
256B THR* 3.2 7.9 + - - -
257B PHE* 3.0 23.7 + - - +
282B ALA* 3.6 10.1 - - + +
285B ALA* 5.1 3.1 - - - -
286B VAL* 4.0 18.2 - - + -
1310B ACP 3.3 41.2 + - + +
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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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166B ASN* 5.7 0.7 - - - -
223B THR* 6.1 0.9 - - - -
253B ALA* 1.3 69.7 - - - +
255B ASP* 1.3 54.9 + - - +
257B PHE* 3.3 9.2 - - - +
258B ASN* 2.7 49.9 + - - -
1310B ACP 2.6 43.0 + - - -
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Residues in contact with ASP 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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43B LYS* 3.5 17.1 - - - +
46B ASN* 2.9 41.2 + - + -
47B GLN* 3.0 38.3 + - + +
50B ALA* 4.0 2.2 - - - +
166B ASN* 4.4 2.1 - - - +
252B ALA* 3.2 11.1 + - - +
253B ALA 3.2 0.4 - - - -
254B GLY* 1.3 76.6 - - - +
256B THR* 1.3 63.8 + - - +
258B ASN 3.3 0.3 + - - -
259B GLY* 3.0 20.6 + - - -
1310B ACP 4.3 4.0 + - - -
1311B RIB 2.6 27.7 + - - -
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Residues in contact with THR 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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46B ASN 5.3 0.4 + - - -
50B ALA* 3.7 14.9 - - + +
252B ALA* 2.9 20.4 + - - +
253B ALA 3.5 4.9 - - - -
255B ASP* 1.3 75.8 - - - +
257B PHE* 1.3 63.1 + - - +
259B GLY* 3.2 2.3 + - - -
260B ALA* 3.0 23.6 + - - +
281B ALA* 3.5 42.2 - - + +
282B ALA* 3.5 4.9 - - - +
285B ALA* 3.6 12.9 - - + +
294B SER* 5.1 0.2 + - - -
295B VAL* 3.9 16.3 - - - +
296B PRO* 3.9 13.5 - - + -
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Residues in contact with PHE 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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185B THR* 4.8 5.2 - - + -
221B LEU* 4.4 10.3 - - + -
223B THR* 4.2 24.7 - - + -
229B VAL* 4.8 7.0 - - + -
253B ALA 3.0 13.6 + - - +
254B GLY* 3.3 11.4 - - - +
256B THR* 1.3 77.5 - - - +
258B ASN* 1.3 69.4 + - - +
261B LEU* 2.8 49.5 + - + +
275B ILE* 4.0 33.2 - - + -
278B ALA* 3.4 41.4 - - + +
279B HIS* 4.0 14.8 - + - -
282B ALA* 4.1 1.7 - - + +
1310B ACP 4.1 20.9 - - - -
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Residues in contact with ASN 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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47B GLN* 3.7 16.9 - - - +
139B LEU* 4.3 11.9 - - + +
165B LEU 5.2 0.2 - - - -
166B ASN* 3.5 32.5 + - - +
185B THR* 2.8 33.8 + - - +
223B THR* 6.1 0.8 - - - +
254B GLY* 2.7 38.9 + - - +
255B ASP 3.7 3.8 - - - +
257B PHE* 1.3 80.5 - - - +
259B GLY* 1.3 64.5 + - - +
261B LEU* 3.4 7.4 + - - +
262B ILE* 3.0 29.5 + - - +
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Residues in contact with GLY 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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47B GLN* 3.8 23.1 - - - +
50B ALA* 3.9 3.8 - - - -
51B ALA* 3.6 14.7 - - - +
139B LEU* 4.4 8.0 - - - +
255B ASP 3.0 13.1 + - - -
256B THR 3.2 2.2 + - - -
258B ASN* 1.3 76.5 - - - +
260B ALA* 1.3 61.9 + - - +
262B ILE* 3.6 1.7 + - - +
263B THR* 3.0 25.5 + - - -
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Residues in contact with ALA 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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50B ALA* 4.4 2.6 - - + +
54B SER* 3.8 17.3 - - - +
256B THR 3.0 15.1 + - - +
259B GLY* 1.3 74.2 - - - +
261B LEU* 1.3 67.1 + - - +
263B THR* 3.5 0.8 - - - -
264B ALA* 3.0 19.8 + - - +
277B PHE* 3.5 32.6 - - + -
278B ALA* 4.0 6.5 - - - -
281B ALA* 3.9 20.9 - - + -
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Residues in contact with LEU 261 (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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183B ILE* 5.0 4.7 - - + -
185B THR* 4.5 10.3 - - + -
221B LEU* 3.5 28.5 - - + -
257B PHE* 2.8 30.6 + - + +
258B ASN* 3.5 6.1 - - - +
260B ALA* 1.3 79.0 - - - +
262B ILE* 1.3 76.5 + - + +
263B THR 3.1 0.3 + - - -
264B ALA* 3.3 1.2 + - - +
265B LEU* 3.1 43.2 + - + +
271B LEU* 4.8 1.1 - - + -
274B ALA* 4.0 24.0 - - + +
275B ILE* 4.2 11.9 - - + -
278B ALA* 3.6 10.4 - - + +
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Residues in contact with ILE 262 (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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7B LEU* 3.6 34.3 - - + -
137B ALA* 4.2 10.1 - - + -
139B LEU* 4.2 19.3 - - + -
164B ALA* 4.0 25.6 - - + -
183B ILE* 4.5 7.0 - - + -
258B ASN* 3.0 16.9 + - - +
259B GLY 4.2 3.4 - - - +
261B LEU* 1.3 93.2 - - + +
263B THR* 1.3 56.8 + - - +
265B LEU* 3.4 14.9 + - + +
266B LEU* 2.9 38.3 + - + +
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Residues in contact with THR 263 (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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7B LEU* 5.5 0.4 - - - +
51B ALA* 3.4 10.2 + - - +
54B SER* 3.8 21.8 + - - +
56B ALA* 3.4 44.0 - - - +
259B GLY 3.0 16.4 + - - -
260B ALA 3.5 8.5 - - - -
261B LEU 3.1 0.6 - - - -
262B ILE* 1.3 76.8 - - - +
264B ALA* 1.3 59.9 + - - +
266B LEU* 3.2 7.3 + - - +
267B GLU* 3.0 43.7 + - + +
277B PHE* 4.7 1.3 - - + -
298B ARG* 4.7 1.1 - - - +
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Residues in contact with ALA 264 (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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260B ALA 3.0 13.7 + - - +
261B LEU 4.0 0.9 - - - +
263B THR* 1.3 80.6 - - - +
265B LEU* 1.3 62.3 + - - +
267B GLU* 3.1 11.0 + - - +
269B LYS* 3.1 50.6 + - + +
274B ALA* 3.7 22.9 - - + +
277B PHE* 3.8 16.1 - - + -
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Residues in contact with LEU 265 (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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183B ILE* 3.9 28.7 - - + -
261B LEU* 3.1 37.9 + - + +
262B ILE* 4.0 9.9 - - + +
264B ALA* 1.3 72.0 - - - +
266B LEU* 1.3 65.8 + - + +
267B GLU 3.0 1.6 - - - -
268B GLU* 2.8 20.1 + - - -
269B LYS 3.9 12.1 - - - +
271B LEU* 4.1 26.9 - - + +
274B ALA* 3.6 22.2 - - + -
218D ARG* 5.1 4.4 + - - +
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Residues in contact with LEU 266 (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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4B ALA* 3.2 29.3 - - + +
5B GLY* 3.5 22.1 + - - +
6B SER 4.3 1.3 - - - +
7B LEU* 3.8 29.8 - - + +
56B ALA* 5.5 4.3 - - + -
136B SER* 4.0 23.1 - - - +
137B ALA* 4.3 12.8 - - + -
162B ILE* 5.1 9.2 - - + -
262B ILE* 2.9 31.0 + - + +
263B THR* 3.2 8.0 + - - +
265B LEU* 1.3 79.3 - - + +
267B GLU* 1.3 59.2 + - - +
268B GLU* 3.1 2.1 + - - +
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Residues in contact with GLU 267 (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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4B ALA* 4.3 13.7 - - + -
55B GLY 4.5 6.6 - - - +
263B THR* 3.0 28.8 + - + +
264B ALA* 3.1 12.1 + - - +
265B LEU 3.0 1.2 - - - -
266B LEU* 1.3 78.7 - - - +
268B GLU* 1.3 70.1 + - - +
269B LYS* 3.2 19.2 + - + +
298B ARG* 2.9 44.5 + - - -
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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