Contacts of the helix formed by residues 308 - 326 (chain A) in PDB entry 4G1U
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 PRO 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 4.1 9.0 - - + +
183A MET* 4.0 31.2 - - + +
184A GLY 3.1 17.9 - - - +
185A SER* 3.8 16.4 - - - -
298A ALA* 4.7 0.5 - - - +
306A GLU 4.1 2.0 - - - +
307A MET* 1.3 94.3 - - + +
309A VAL* 1.3 65.6 + - - +
310A GLY 3.3 0.8 + - - +
311A LEU* 3.3 23.9 + - + +
312A LEU* 4.0 1.2 + - - +
168B TYR* 3.8 28.7 - - + +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 5.7 0.2 - - - +
184A GLY 2.8 11.8 + - - +
185A SER* 4.2 1.1 - - - +
186A LEU* 4.2 17.0 - - + +
257A ILE* 4.6 7.6 - - + -
291A LEU* 3.6 30.3 - - + -
294A ALA* 4.1 16.8 - - + -
295A ASP* 3.3 36.1 - - - +
298A ALA* 4.5 9.6 - - + -
307A MET 3.6 0.8 + - - -
308A PRO* 1.3 71.4 - - - +
310A GLY* 1.3 53.9 + - - +
312A LEU* 2.7 29.6 + - - +
313A THR* 3.0 20.6 + - + -
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Residues in contact with GLY 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A MET 3.5 17.5 - - - -
184A GLY* 3.1 9.6 + - - -
256A VAL 4.5 9.2 - - - -
257A ILE* 4.8 3.3 - - - +
308A PRO 3.2 0.2 - - - -
309A VAL* 1.3 74.7 - - - +
311A LEU* 1.3 60.3 + - - +
312A LEU 3.2 0.2 - - - -
313A THR* 3.7 12.1 - - - -
314A SER* 2.7 36.4 + - - -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A MET* 4.5 19.1 + - + +
307A MET* 4.6 6.3 - - + -
308A PRO* 3.3 36.2 + - + +
309A VAL 3.2 0.8 - - - -
310A GLY* 1.3 75.7 - - - +
312A LEU* 1.3 60.4 + - - +
314A SER* 6.0 0.2 - - - -
315A LEU* 2.9 31.4 + - - +
160B GLY 4.4 3.1 - - - +
161B ALA* 3.4 33.2 - - - +
164B GLY* 3.6 14.6 - - - +
165B VAL* 3.5 38.2 - - + +
168B TYR* 4.2 8.3 - - + -
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA* 3.6 30.7 - - + +
297A LEU* 4.1 22.9 - - + +
298A ALA* 3.8 23.1 - - + +
301A LEU* 4.5 15.3 - - + -
307A MET* 4.4 20.4 - - + -
308A PRO 4.0 0.4 + - - +
309A VAL* 2.7 19.5 + - - +
311A LEU* 1.3 75.5 - - - +
313A THR* 1.3 58.0 + - - +
315A LEU* 4.4 18.6 - - + -
316A LEU* 2.9 46.2 + - + +
165B VAL* 5.1 2.7 - - + -
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Residues in contact with THR 313 (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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257A ILE* 3.2 35.8 - - + +
258A GLY 4.2 6.2 + - - -
259A PHE* 3.8 17.8 - - - +
260A ILE* 4.3 17.0 - - + -
294A ALA* 4.3 11.7 - - + -
309A VAL* 3.0 24.3 + - + +
310A GLY* 3.5 8.7 + - - -
312A LEU* 1.3 73.1 - - - +
314A SER* 1.3 63.7 + - - +
316A LEU* 5.0 2.0 - - - -
317A GLY* 2.8 32.4 + - - +
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Residues in contact with SER 314 (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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258A GLY 5.8 1.0 + - - -
259A PHE* 4.0 14.7 - - - -
310A GLY* 2.7 23.2 + - - -
311A LEU* 6.0 0.2 - - - -
313A THR* 1.3 78.0 + - - +
315A LEU* 1.3 59.3 + - - +
318A GLY* 2.9 28.4 + - - -
319A PRO* 4.4 0.2 - - - +
157B ALA* 3.9 23.4 - - - +
161B ALA* 3.7 17.5 - - - -
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU 2.9 20.1 + - - +
312A LEU* 3.8 20.2 - - + +
314A SER* 1.3 77.2 - - - +
316A LEU* 1.3 67.8 + - + +
319A PRO* 2.9 29.8 - - - +
158B LEU* 3.6 38.1 - - + +
161B ALA* 3.5 6.4 - - + +
162B ALA* 4.5 13.9 - - + +
165B VAL* 4.7 15.0 - - + -
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Residues in contact with LEU 316 (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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290A LEU* 6.6 0.4 - - + -
294A ALA* 5.8 8.1 - - + -
297A LEU* 5.2 14.4 - - + -
312A LEU* 2.9 36.9 + - + +
313A THR* 4.4 2.0 - - - +
315A LEU* 1.3 85.5 - - + +
317A GLY* 1.3 63.3 + - - +
319A PRO* 3.5 9.2 - - - +
320A TYR* 3.5 16.2 + - - +
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 3.3 24.7 - - - -
263A VAL* 4.8 6.3 - - - -
313A THR 2.8 20.9 + - - -
316A LEU* 1.3 72.3 - - - +
318A GLY* 1.3 65.6 + - - +
320A TYR* 3.6 8.3 - - - +
321A PHE* 3.0 22.3 + - - +
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Residues in contact with GLY 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 3.7 11.7 - - - -
314A SER 2.9 18.7 + - - -
317A GLY* 1.3 73.4 - - - +
319A PRO* 1.3 59.1 - - - +
321A PHE* 2.8 25.5 + - - +
322A LEU 3.0 10.2 + - - -
154B ALA* 3.5 25.8 - - - +
157B ALA* 5.0 0.7 - - - -
158B LEU 5.0 1.3 - - - -
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Residues in contact with PRO 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER 4.4 0.2 - - - +
315A LEU 2.9 25.8 - - - +
316A LEU* 3.5 6.1 - - - +
318A GLY* 1.3 82.8 - - - +
320A TYR* 1.3 63.1 + - - +
322A LEU* 3.9 18.3 - - + +
323A TRP* 3.2 19.9 + - - +
154B ALA* 4.7 1.3 - - + +
158B LEU* 4.2 27.8 - - + -
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Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 6.1 1.3 - - + -
263A VAL* 3.6 46.5 - - + +
266A HIS* 4.9 10.5 - + + +
267A LEU* 4.0 19.5 - - + +
270A MET* 5.3 6.2 - - - +
316A LEU 3.5 17.5 - - - +
317A GLY* 3.6 5.4 - - - +
318A GLY 3.0 0.4 - - - -
319A PRO* 1.3 82.6 - - - +
321A PHE* 1.3 65.6 + + + +
323A TRP* 3.0 49.1 + + - +
324A LEU* 3.0 20.6 + - + +
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Residues in contact with PHE 321 (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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84A LEU* 3.6 29.6 - - + -
89A LEU* 5.2 9.6 - - + -
149A LEU* 5.3 0.9 - - + -
259A PHE* 4.2 10.3 - + + -
262A LEU* 3.4 24.2 - - + -
317A GLY 3.0 13.2 + - - +
318A GLY 2.8 9.9 + - - +
320A TYR* 1.3 82.5 - + + +
322A LEU* 1.3 61.0 + - - -
324A LEU* 3.2 26.4 + - + +
325A ILE* 3.3 20.9 + - + +
150B LEU* 3.5 50.3 - - + -
153B ILE* 5.0 7.4 - - + -
154B ALA* 3.8 19.7 - - + -
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Residues in contact with LEU 322 (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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318A GLY 3.0 6.7 + - - +
319A PRO* 4.0 15.3 - - + +
321A PHE* 1.3 77.3 - - - +
323A TRP* 1.3 60.7 + - - +
325A ILE* 3.6 7.3 - - + +
326A LEU* 3.1 25.7 + - + +
133B ILE* 5.3 16.6 - - + -
137B LEU* 5.0 10.5 - - + -
151B ALA* 3.6 36.6 - - + +
154B ALA* 3.7 15.6 - - + +
155B ILE* 4.1 24.5 - - + -
158B LEU* 6.4 1.1 - - + -
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Residues in contact with TRP 323 (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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270A MET* 5.5 9.4 - - + -
319A PRO 3.2 13.2 + - - +
320A TYR* 3.0 43.6 + + - +
322A LEU* 1.3 78.2 - - - +
324A LEU* 1.3 103.2 + - + +
326A LEU* 3.2 24.7 - - + +
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Residues in contact with LEU 324 (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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84A LEU* 4.8 7.6 - - + -
262A LEU* 6.0 0.9 - - + -
266A HIS* 4.4 24.2 - - + +
270A MET* 4.8 16.4 - - + -
320A TYR* 3.0 20.1 + - + +
321A PHE* 3.2 31.2 + - + +
323A TRP* 1.3 98.2 - - + +
325A ILE* 1.3 70.0 + - + +
326A LEU 4.0 4.0 - - - +
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Residues in contact with ILE 325 (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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84A LEU* 5.4 2.0 - - + -
321A PHE* 3.3 24.2 + - + +
322A LEU* 3.6 11.4 - - + +
324A LEU* 1.3 82.3 - - + +
326A LEU* 1.3 60.6 + - - +
137B LEU* 4.1 17.9 - - + -
147B ARG* 2.9 63.1 + - + +
150B LEU* 3.8 39.9 - - + -
151B ALA* 5.0 6.5 - - + +
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Residues in contact with LEU 326 (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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322A LEU* 3.1 19.8 + - + +
323A TRP* 3.2 20.2 - - - +
324A LEU 3.3 4.1 - - - +
325A ILE* 1.3 82.3 - - - +
133B ILE* 5.7 8.1 - - + -
136B THR* 5.8 1.6 - - + -
137B LEU* 3.6 35.7 - - + -
147B ARG* 4.7 6.1 + - - +
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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
------------------------------------------------------------
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