Contacts of the helix formed by residues 251 - 265 (chain B) in PDB entry 2GFP
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 LEU 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B ILE 3.4 7.3 + - - +
248B LEU* 4.4 15.7 - - + +
250B ILE* 1.3 84.1 - - + +
252B PRO* 1.3 76.9 - - + +
254B PRO* 2.9 25.7 - - + +
255B ALA* 3.3 10.9 + - + +
297B MET* 5.2 6.7 - - + -
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Residues in contact with PRO 252 (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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248B LEU* 2.6 32.5 - - + +
249B PHE 4.3 2.0 - - - +
251B LEU* 1.3 92.5 - - + +
253B ILE* 1.3 51.3 + - - +
255B ALA* 3.3 11.2 - - + +
256B ALA* 2.6 35.7 + - - +
297B MET* 4.6 11.4 - - + +
300B TRP* 4.4 4.5 - - + -
301B THR* 3.1 48.6 - - + +
305B PRO* 6.0 0.2 - - - -
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Residues in contact with ILE 253 (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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132B HIS* 4.7 3.4 - - + -
133B ALA* 3.7 25.4 - - + +
136B LEU* 3.5 43.5 - - + +
137B LEU* 3.8 15.9 - - + +
249B PHE 3.2 15.6 + - - +
250B ILE* 2.8 33.0 + - + +
251B LEU 3.0 2.4 + - - -
252B PRO* 1.3 73.1 - - - +
254B PRO* 1.4 71.6 - - + +
256B ALA* 2.8 17.0 + - + +
257B PHE* 3.1 9.7 + - - +
300B TRP* 3.8 12.1 - - + -
304B VAL* 3.6 14.6 - - + -
308B LEU* 6.0 0.2 - - + -
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Residues in contact with PRO 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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133B ALA* 4.4 9.6 - - + -
137B LEU* 4.3 12.8 - - + -
250B ILE 2.6 30.5 - - - +
251B LEU* 2.9 22.0 - - + +
253B ILE* 1.4 79.1 - - + +
255B ALA* 1.3 55.7 + - - +
257B PHE* 2.9 32.6 + - + +
258B PHE* 3.5 8.0 + - - -
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Residues in contact with ALA 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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251B LEU* 3.5 14.1 - - + +
252B PRO* 3.3 15.3 - - + +
253B ILE 3.0 0.2 - - - -
254B PRO* 1.3 82.0 - - + +
256B ALA* 1.3 50.9 + - - +
258B PHE* 3.6 5.8 + - - +
259B GLY* 2.6 31.2 + - - -
301B THR* 5.9 2.7 - - + -
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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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252B PRO 2.6 16.8 + - - +
253B ILE* 2.8 17.9 + - + +
255B ALA* 1.3 71.0 - - - +
257B PHE* 1.3 55.7 + - - +
259B GLY* 3.1 8.7 - - - +
260B ALA* 2.6 31.9 + - - +
301B THR* 6.4 0.2 - - - -
304B VAL* 3.9 12.1 - - + -
305B PRO* 3.5 32.7 - - + +
308B LEU* 3.7 7.3 - - + +
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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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129B GLN* 4.0 16.2 - - + -
130B LEU* 4.4 4.0 - - + -
131B ARG* 3.4 47.4 - - + +
132B HIS 4.5 1.1 - - - -
133B ALA* 4.1 23.1 - - + +
134B ASN* 5.4 1.6 - - - -
253B ILE* 3.1 4.9 + - - +
254B PRO* 2.9 20.3 + - + +
256B ALA* 1.3 81.7 - - - +
258B PHE* 1.3 87.4 + + + +
260B ALA* 3.0 16.4 + - - +
261B TRP* 3.6 33.9 + + - -
308B LEU* 5.1 4.0 - - - -
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Residues in contact with PHE 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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254B PRO 3.5 7.0 + - - +
255B ALA* 3.6 6.1 - - - +
257B PHE* 1.3 106.3 - + + +
259B GLY* 1.3 57.3 + - - +
261B TRP* 3.2 38.0 + + - +
262B PHE* 2.8 25.1 + - - +
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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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255B ALA 2.6 24.0 + - - -
256B ALA* 3.3 7.9 - - - -
257B PHE 2.9 0.8 - - - -
258B PHE* 1.3 73.9 - - - +
260B ALA* 1.3 53.5 + - - +
262B PHE* 3.1 13.1 + - - +
263B ALA* 2.6 31.4 + - - +
268B LYS* 3.9 7.6 - - - +
305B PRO* 4.1 7.5 - - - +
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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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131B ARG* 5.8 3.6 - - + -
256B ALA 2.6 8.6 + - - -
257B PHE* 3.0 10.1 + - - +
259B GLY* 1.3 71.0 - - - +
261B TRP* 1.3 70.1 + - + +
263B ALA* 2.8 31.6 + - - +
264B GLY 3.3 2.8 + - - -
305B PRO* 4.8 4.0 - - - -
308B LEU* 3.3 36.6 - - + -
309B PHE* 5.2 3.9 - - + +
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Residues in contact with TRP 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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129B GLN* 4.6 15.3 - - - -
131B ARG* 4.1 33.2 - - + +
257B PHE* 3.7 43.2 + + - -
258B PHE* 3.4 48.7 - + - +
260B ALA* 1.3 82.4 - - + +
262B PHE* 1.3 57.5 + - - +
264B GLY* 3.3 5.4 + - - -
265B ARG* 3.1 17.8 + - - +
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Residues in contact with PHE 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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258B PHE 2.8 14.7 + - - +
259B GLY* 3.1 15.9 - - - +
260B ALA 3.0 0.2 - - - -
261B TRP* 1.3 74.6 - - - +
263B ALA* 1.3 54.7 + - - +
264B GLY 2.9 1.8 - - - -
265B ARG* 2.4 79.6 + - + +
268B LYS* 3.7 21.1 - - + -
270B PHE* 3.2 36.8 - + + -
271B SER* 3.1 33.7 - - - -
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Residues in contact with ALA 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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259B GLY 2.6 13.6 + - - +
260B ALA* 2.8 20.4 - - - +
262B PHE* 1.3 68.5 - - - +
264B GLY* 1.3 68.9 + - - +
267B ASN* 3.0 9.9 + - - -
268B LYS* 2.6 39.1 + - + +
305B PRO 4.6 0.7 - - - +
309B PHE* 4.0 34.4 - - + -
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Residues in contact with GLY 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 3.3 3.4 + - - -
261B TRP* 3.3 8.7 + - - -
262B PHE 2.9 0.6 - - - -
263B ALA* 1.3 86.1 - - - +
265B ARG* 1.3 51.4 + - - +
266B PRO 3.1 0.7 - - - -
267B ASN* 2.6 31.5 + - - -
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Residues in contact with ARG 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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261B TRP 3.1 6.9 + - - +
262B PHE* 2.4 72.6 + - + +
264B GLY* 1.3 67.7 - - - +
266B PRO* 1.4 80.0 - - + +
267B ASN 2.5 19.1 + - - +
268B LYS* 3.0 1.6 + - - -
270B PHE* 5.9 0.2 - - - -
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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