Contacts of the helix formed by residues 125 - 129 (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 ALA 125 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234 GLY 3.5 3.8 + - - -
1244 VAL* 1.3 84.1 - - - +
1264 ALA* 1.3 66.0 + - - +
1274 GLN 3.2 0.9 + - - -
1284 HIS 3.3 2.6 + - - -
1294 SER* 2.9 22.1 + - - -
3024 MET* 3.1 13.1 - - - +
3034 PRO 4.2 12.0 + - - -
3044 TYR* 4.6 8.2 - - + +
3094 GLU* 5.5 0.4 + - - -
1205 LYS 4.9 2.5 - - - +
1215 GLY 3.6 24.7 - - - +
1245 MET* 4.9 2.5 - - + -
1255 HIS* 3.8 16.4 - - + +
1036 MET* 5.4 0.7 - - + -
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Residues in contact with ALA 126 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254 ALA* 1.3 78.2 - - - +
1274 GLN* 1.3 61.4 + - - +
1284 HIS 3.1 2.2 + - - -
1294 SER* 3.8 6.0 + - - -
1304 GLN 4.5 2.9 + - - -
2664 TRP* 5.8 0.7 - - - -
3014 PRO* 3.8 26.7 - - + -
3024 MET* 2.8 23.9 + - - +
996 LYS* 3.2 25.7 + - + -
1026 TYR* 5.7 0.2 - - + -
1036 MET* 3.8 25.5 - - + +
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Residues in contact with GLN 127 (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* 3.5 20.0 - - - +
1244 VAL 4.5 0.4 + - - -
1254 ALA 3.2 1.2 + - - -
1264 ALA* 1.3 77.8 - - - +
1284 HIS* 1.3 78.1 + - + +
1294 SER 3.7 0.9 - - - -
1255 HIS* 3.1 25.4 + - + -
1355 ASN* 4.0 8.5 + - - +
1365 GLY* 3.0 31.1 + - - +
1375 ILE* 3.7 15.4 + - + +
956 ASN* 2.7 54.4 + - - +
966 SER* 4.9 1.4 + - - +
996 LYS* 4.8 2.0 - - + -
1036 MET* 3.8 16.2 - - + +
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Residues in contact with HIS 128 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824 THR* 5.3 5.9 - - + +
844 ASN* 3.3 22.1 + - - +
854 PHE* 3.7 30.3 - + - -
1194 GLY 4.1 6.1 - - - +
1214 SER* 4.5 2.8 - - - -
1244 VAL* 3.3 31.6 + - + +
1254 ALA 3.3 1.2 + - - -
1264 ALA 3.1 0.4 - - - -
1274 GLN* 1.3 105.9 - - + +
1294 SER* 1.3 60.2 + - - +
615 PHE* 3.5 28.7 - + - -
1245 MET* 3.7 24.6 - - + +
1365 GLY* 3.7 28.9 + - - -
1375 ILE* 4.5 0.2 - - + -
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Residues in contact with SER 129 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844 ASN* 3.6 0.2 + - - -
1194 GLY 3.8 7.2 - - - -
1204 ALA* 3.2 21.7 + - - +
1214 SER 4.3 4.2 + - - -
1244 VAL* 3.5 13.0 - - - +
1254 ALA 2.9 22.6 + - - -
1264 ALA 3.8 3.4 + - - -
1274 GLN 3.7 0.4 - - - -
1284 HIS* 1.3 82.2 - - - +
1304 GLN* 1.3 67.4 + - - +
1314 CYS* 3.7 0.9 + - - +
3024 MET* 3.4 40.9 - - - +
3094 GLU* 4.8 1.4 + - - -
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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