Contacts of the helix formed by residues 307 - 318 (chain A) in PDB entry 4IX8
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 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A PRO* 4.2 8.1 - - + -
300A LEU* 4.1 8.3 - - + +
302A ASP* 2.8 19.0 + - - +
306A VAL* 1.3 82.2 - - - +
308A GLY* 1.3 63.7 + - - +
309A ASP 3.2 2.9 - - - -
310A TRP* 2.9 29.6 + - + +
311A ALA* 3.2 10.7 + - - +
44B ILE* 4.0 28.3 - - + -
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Residues in contact with GLY 308 (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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300A LEU* 5.5 0.9 - - - -
302A ASP* 3.8 3.0 + - - -
305A ASN* 3.7 20.1 + - - -
306A VAL 3.6 1.4 - - - -
307A ALA* 1.3 77.1 - - - +
309A ASP* 1.3 58.2 + - - +
311A ALA* 3.2 8.6 + - - +
312A VAL* 2.9 34.2 + - - +
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Residues in contact with ASP 309 (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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307A ALA 3.2 1.0 - - - -
308A GLY* 1.3 73.7 - - - +
310A TRP* 1.3 60.5 + - - +
312A VAL* 3.8 9.1 - - - +
313A GLY 2.9 24.1 + - - -
43B ARG* 4.2 19.5 + - - -
44B ILE 3.8 16.4 + - - +
45B ALA* 4.2 7.6 - - - +
46B SER* 3.6 26.7 + - - +
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Residues in contact with TRP 310 (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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157A ALA 3.0 27.6 + - - -
160A ALA* 4.1 8.7 - - + -
161A LEU* 3.5 33.6 - - + +
249A PRO* 3.7 29.8 - - + -
251A ILE* 3.8 20.2 - - + -
277A PRO* 5.2 1.8 - - + -
279A LEU* 3.6 43.5 - - + -
300A LEU* 4.2 19.7 - - + -
307A ALA* 2.9 25.1 + - + +
309A ASP* 1.3 75.7 - - - +
311A ALA* 1.3 64.3 + - - +
313A GLY* 3.1 2.6 + - - -
314A MET* 2.9 40.2 + - + +
44B ILE* 4.1 12.9 + - + -
46B SER* 4.5 7.8 - - - +
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Residues in contact with ALA 311 (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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143A ASN* 5.3 6.7 - - - +
145A ILE* 4.6 2.7 - - + +
300A LEU* 3.8 24.6 - - + +
307A ALA 3.2 3.3 + - - +
308A GLY* 3.5 11.9 - - - +
310A TRP* 1.3 80.8 - - - +
312A VAL* 1.3 63.5 + - + +
314A MET* 3.2 16.5 + - + +
315A GLU* 3.0 34.6 + - - +
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Residues in contact with VAL 312 (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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308A GLY 2.9 21.4 + - - +
309A ASP* 3.8 8.3 - - - +
311A ALA* 1.3 75.8 - - + +
313A GLY* 1.3 56.9 + - - +
315A GLU* 3.3 14.8 + - - +
316A ARG* 2.9 60.1 + - + +
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Residues in contact with GLY 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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160A ALA* 3.8 10.1 - - - -
309A ASP 2.9 16.6 + - - -
310A TRP 3.1 3.8 + - - -
312A VAL* 1.3 76.6 - - - +
314A MET* 1.3 62.3 + - - +
316A ARG* 3.2 8.5 + - - +
317A LEU* 3.0 26.9 + - - +
46B SER* 4.5 3.6 - - - -
50B ALA* 3.7 21.7 - - - +
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Residues in contact with MET 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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145A ILE* 3.7 18.6 - - + -
153A ALA 5.4 0.4 - - - +
156A LEU* 3.5 16.5 - - + +
157A ALA* 3.7 25.4 - - - -
160A ALA* 3.5 19.7 - - + +
279A LEU* 3.6 35.0 - - + -
298A SER* 4.6 8.1 - - - +
300A LEU* 5.1 5.6 - - + -
310A TRP* 2.9 33.3 + - + +
311A ALA* 3.7 16.4 - - + +
313A GLY* 1.3 73.9 - - - +
315A GLU* 1.3 63.9 + - - +
317A LEU* 3.0 15.5 + - - +
318A THR* 3.0 18.2 + - - +
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Residues in contact with GLU 315 (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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112A THR* 4.4 0.3 + - - -
113A VAL* 3.9 32.3 - - + +
119A ARG* 5.3 4.0 + - - -
142A GLU 4.7 9.6 - - - +
145A ILE* 4.1 13.5 - - + -
311A ALA* 3.0 26.4 + - - +
312A VAL* 3.4 16.1 - - + +
314A MET* 1.3 77.0 - - - +
316A ARG* 1.3 62.3 + - + +
318A THR* 2.7 24.7 + - - -
319A GLN* 4.0 4.2 + - - +
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Residues in contact with ARG 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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312A VAL* 2.9 40.5 + - + +
313A GLY* 3.5 7.9 - - - +
315A GLU* 1.3 77.7 - - + +
317A LEU* 1.3 58.0 + - - +
319A GLN* 3.1 42.7 + - - +
50B ALA 3.5 15.3 - - - +
51B GLN* 2.8 37.2 + - - +
53B THR* 3.4 27.1 - - - +
54B LEU* 3.7 17.7 - - - +
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Residues in contact with LEU 317 (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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152A GLN* 5.0 1.6 + - - -
156A LEU* 3.5 25.9 - - + +
159A THR* 3.5 29.6 - - - +
160A ALA* 3.8 28.7 - - + +
313A GLY 3.0 12.2 + - - +
314A MET 3.0 4.4 + - - +
316A ARG* 1.3 72.5 - - - +
318A THR* 1.3 59.6 + - - +
319A GLN 3.0 6.3 + - - -
320A LEU* 3.2 29.9 + - + +
321A ILE 4.8 0.5 + - - -
49B HIS* 3.6 23.6 - - + +
50B ALA* 4.0 11.4 - - + -
53B THR* 3.5 26.5 - - - +
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Residues in contact with THR 318 (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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112A THR* 2.8 42.4 + - - +
113A VAL* 3.4 7.6 - - + +
145A ILE* 3.9 26.5 - - + -
146A ILE 5.0 1.8 - - - +
152A GLN* 4.7 8.5 - - - +
156A LEU* 3.9 16.2 - - + -
314A MET 3.0 14.7 + - - +
315A GLU* 2.7 17.0 + - - +
317A LEU* 1.3 76.4 - - - +
319A GLN* 1.3 62.5 + - - +
320A LEU 3.1 1.3 + - - -
321A ILE* 3.8 2.6 + - - +
322A ALA* 3.2 18.9 + - - -
323A GLY* 3.8 4.0 + - - -
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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