Contacts of the helix formed by residues 132 - 137 (chain 6) in PDB entry 3EXG
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 PHE 132 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836 PHE* 3.7 22.4 - - + -
846 ASN* 3.7 10.8 - - - -
866 SER* 5.2 0.4 - - - -
876 MET* 3.5 39.9 - - + -
1186 ASN* 3.0 22.9 - - - +
1306 GLN* 3.4 43.5 - - + -
1316 CYS* 1.3 75.5 - - - +
1336 ALA* 1.3 66.3 + - - +
1346 ALA* 3.3 2.0 - - - -
1356 TRP* 3.8 30.1 - + + +
1366 TYR* 3.2 51.1 + + + +
1706 LEU* 4.0 5.2 - - + -
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Residues in contact with ALA 133 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1316 CYS* 3.2 20.5 - - - -
1326 PHE* 1.3 76.2 - - - +
1346 ALA* 1.3 57.8 + - - +
1366 TYR* 4.3 0.5 - - - +
1376 GLY* 2.9 30.1 + - - -
1446 VAL* 4.8 0.3 - - - +
1706 LEU* 3.5 19.1 - - + +
2126 HIS* 3.8 16.4 - - + +
2416 ILE* 3.7 13.7 - - + +
2716 VAL* 3.7 22.9 - - + -
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Residues in contact with ALA 134 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354 TRP* 5.3 0.2 - - - -
1384 HIS* 3.9 19.1 - - + +
2694 PHE* 4.0 15.1 - - + +
1316 CYS* 4.9 1.6 - - - +
1326 PHE* 3.3 0.6 - - - -
1336 ALA* 1.3 77.2 - - - +
1356 TRP* 1.3 68.1 + - + +
1376 GLY* 3.4 6.9 + - - -
1386 HIS* 3.6 11.8 + - - +
2636 GLU* 5.8 0.4 - - - +
2696 PHE 3.6 23.6 - - - +
2706 GLY* 3.9 17.5 - - - -
2716 VAL* 4.0 7.4 - - + +
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Residues in contact with TRP 135 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904 ILE* 4.0 23.8 - - + -
944 ILE* 4.1 14.8 - - + -
1344 ALA 4.9 0.4 - - - -
1354 TRP* 3.0 83.9 + + + +
1364 TYR* 5.4 0.7 - - - -
1384 HIS* 3.6 26.2 + + + -
1394 CYS* 3.7 23.6 - - - -
876 MET* 4.1 12.6 - - + -
906 ILE* 4.2 12.6 - - + -
1306 GLN* 4.3 11.0 - - - -
1316 CYS 6.0 0.7 - - - -
1326 PHE* 3.5 41.3 + + + +
1346 ALA* 1.3 79.3 - - - +
1366 TYR* 1.3 59.8 + - + +
1386 HIS* 3.0 21.8 + - - +
1396 CYS* 3.9 1.0 - - - -
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Residues in contact with TYR 136 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354 TRP* 5.7 0.2 - + - -
836 PHE* 3.8 22.0 - + - -
866 SER* 3.0 25.3 + - - -
906 ILE* 3.4 40.0 - - + +
936 VAL* 4.1 18.3 - - + +
946 ILE* 4.6 4.7 - - + -
1326 PHE* 3.2 49.1 + + + +
1356 TRP* 1.3 75.5 - - - +
1376 GLY* 1.3 59.1 + - - +
1386 HIS 2.8 11.9 + - - -
1396 CYS* 3.5 10.4 + - - +
1426 LEU* 3.9 26.9 - - + +
1446 VAL* 3.4 29.1 - - + +
1686 VAL* 4.2 16.8 - - + -
1706 LEU* 4.5 2.5 - - + -
2426 ARG* 4.7 0.2 - - - -
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Residues in contact with GLY 137 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2684 GLN* 4.9 0.2 - - - -
2694 PHE* 2.8 34.7 - - - -
1336 ALA 2.9 19.7 + - - -
1346 ALA 3.4 0.4 + - - -
1356 TRP 3.3 1.0 - - - -
1366 TYR* 1.3 74.3 - - - +
1386 HIS* 1.3 56.0 + - - +
1396 CYS 3.6 0.9 - - - -
1446 VAL* 4.0 7.6 - - - -
2416 ILE* 3.9 11.4 - - - -
2426 ARG* 3.1 25.2 + - - -
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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
------------------------------------------------------------
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