Contacts of the helix formed by residues 82 - 88 (chain 4) 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 THR 82 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374 TYR* 3.5 20.6 - - - +
804 PHE* 3.6 16.8 - - - +
814 MET* 1.3 88.1 - - + +
834 PHE* 1.3 63.4 + - - +
844 ASN* 2.8 29.1 + - - +
854 PHE* 3.0 39.1 + - + +
1174 PRO* 3.3 16.2 - - + -
1284 HIS* 5.2 6.4 - - + +
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Residues in contact with PHE 83 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804 PHE* 4.1 18.2 - + + -
824 THR* 1.3 70.3 - - - +
844 ASN* 1.3 60.1 + - - +
854 PHE 3.1 0.2 - - - -
864 SER* 2.6 41.0 + - - +
1144 PHE* 4.1 17.5 - - + -
1154 ARG* 3.8 2.5 - - - -
1164 GLY* 3.3 29.2 - - - -
1174 PRO 2.8 12.9 + - - +
1184 ASN* 3.8 10.9 - - + +
1324 PHE* 3.4 23.0 - - + -
1364 TYR* 3.6 26.9 - + - -
1684 VAL* 3.5 32.8 - - + -
1694 VAL 3.2 23.3 - - - -
1704 LEU* 3.7 13.2 - - + -
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Residues in contact with ASN 84 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824 THR* 2.8 25.4 + - - +
834 PHE* 1.3 76.8 - - - +
854 PHE* 1.3 69.0 + - + +
864 SER 3.2 0.7 + - - -
874 MET* 3.2 27.2 + - + +
884 GLN 4.8 0.3 + - - -
1184 ASN* 6.2 0.6 - - - +
1194 GLY 5.5 2.4 + - - +
1274 GLN 3.5 23.3 - - - +
1284 HIS* 3.3 26.0 + - - +
1294 SER 3.6 1.8 + - - +
1304 GLN* 3.3 38.0 + - - +
1324 PHE* 3.6 11.7 - - - -
1375 ILE* 4.8 3.5 - - + +
916 ASP* 5.2 1.0 - - - +
956 ASN* 4.7 6.0 + - - +
996 LYS* 5.3 1.0 + - - -
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Residues in contact with PHE 85 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284 GLU* 5.3 1.3 - - - -
594 GLU* 3.6 41.3 - - + +
804 PHE* 4.4 3.6 - - + -
814 MET* 3.6 22.9 - - + +
824 THR* 3.0 47.1 + - + +
844 ASN* 1.3 75.3 - - + +
864 SER* 1.3 62.6 + - - +
874 MET 3.2 1.3 + - - -
884 GLN* 3.6 14.5 + - - +
1284 HIS* 3.7 30.1 - + - -
1365 GLY 4.2 5.8 - - - -
1375 ILE* 3.3 37.2 - - + -
1385 VAL* 5.2 5.6 - - + -
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Residues in contact with SER 86 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804 PHE* 3.8 28.7 - - - -
824 THR 3.8 2.0 + - - -
834 PHE* 2.6 35.6 + - - -
854 PHE* 1.3 77.0 - - - +
874 MET* 1.3 60.0 + - - +
894 ALA* 2.6 27.4 + - - -
904 ILE* 3.0 10.1 + - - +
1324 PHE* 4.8 1.2 - - - -
1364 TYR* 2.7 30.4 + - - -
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Residues in contact with MET 87 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844 ASN* 3.2 15.4 + - + +
854 PHE 3.2 1.4 - - - -
864 SER* 1.3 82.6 + - - +
884 GLN* 1.3 61.0 + - - +
894 ALA 3.0 1.8 + - - -
904 ILE* 3.3 23.5 + - + +
1304 GLN* 4.4 2.9 - - - +
1324 PHE* 3.6 31.6 - - + -
1354 TRP* 3.9 24.0 - - + -
876 MET 4.2 3.8 - - - +
886 GLN 5.0 0.9 - - - +
906 ILE* 4.0 19.8 - - + +
916 ASP* 4.1 13.4 + - + +
946 ILE* 3.9 29.2 - - + -
956 ASN* 3.2 38.1 - - - +
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Residues in contact with GLN 88 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1773 GLU* 5.3 1.6 + - - -
594 GLU* 3.6 20.6 + - + +
604 MET* 3.4 35.8 - - + +
844 ASN 6.0 0.2 - - - +
854 PHE* 3.6 13.9 + - - +
864 SER 2.9 1.0 + - - -
874 MET* 1.3 75.9 - - - +
894 ALA* 1.3 57.1 + - - +
904 ILE 3.6 0.2 - - - -
1375 ILE* 3.6 22.3 - - + +
1385 VAL 3.8 3.0 - - - +
1725 GLN* 3.4 30.6 + - - +
1745 GLN* 3.3 19.8 + - - -
606 MET* 3.6 28.1 - - + +
876 MET 5.8 0.4 - - - -
886 GLN 5.1 1.8 - - - -
916 ASP* 4.0 14.0 - - + +
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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