Contacts of the helix formed by residues 305 - 311 (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 ALA 305 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113 GLY* 4.3 11.4 - - - +
1193 GLY 3.0 14.5 + - - +
3293 GLU* 4.4 2.5 - - - +
3303 PRO* 3.6 38.6 - - + -
3046 TYR* 1.3 79.4 - - - +
3066 LYS* 1.3 66.6 + - - +
3076 ILE* 4.3 2.0 - - + +
3086 LEU* 3.9 14.5 - - + +
3096 GLU* 2.7 21.1 + - - +
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Residues in contact with LYS 306 (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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593 ARG* 3.6 47.5 - - - +
3293 GLU* 3.7 14.8 + - - +
3046 TYR 3.1 3.8 + - - -
3056 ALA* 1.3 69.7 - - - +
3076 ILE* 1.3 57.7 + - - +
3096 GLU* 3.2 0.5 + - - +
3106 ASP* 2.8 70.1 + - - +
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Residues in contact with ILE 307 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3293 GLU* 3.4 33.6 + - + +
3303 PRO 3.7 23.3 - - - +
3323 LEU* 4.4 13.6 - - + +
3056 ALA* 3.1 3.5 - - + -
3066 LYS* 1.3 77.7 - - - +
3086 LEU* 1.3 81.2 + - + +
3106 ASP* 3.5 5.7 + - + +
3116 ASN* 2.7 36.7 + - - +
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Residues in contact with LEU 308 (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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1183 LYS 5.1 0.4 - - - +
1193 GLY 5.2 0.7 - - - +
1203 LYS* 3.7 36.3 - - + -
3303 PRO* 3.7 22.2 - - + -
3313 PRO 4.1 5.2 - - - +
3323 LEU* 3.9 29.8 - - + -
3343 GLU 4.7 1.1 - - - +
3353 LEU* 3.8 28.6 - - + +
3036 PRO* 3.6 20.9 - - + -
3056 ALA* 3.0 17.0 + - + +
3076 ILE* 1.3 86.4 - - + +
3096 GLU* 1.3 63.6 + - - +
3116 ASN* 3.2 9.4 + - - +
3126 SER* 2.9 17.2 + - - -
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Residues in contact with GLU 309 (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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593 ARG* 3.2 15.0 + - - +
1216 SER 3.8 6.5 - - - +
1226 ALA* 3.3 10.6 - - - +
1236 GLY* 2.7 41.6 + - - -
1246 VAL* 4.2 1.4 + - - -
1256 ALA 4.6 0.3 + - - -
1296 SER* 5.8 0.6 + - - -
3026 MET* 3.8 21.9 - - - +
3036 PRO* 3.2 28.4 - - - +
3046 TYR 3.9 1.7 - - - +
3056 ALA 2.7 16.7 + - - +
3066 LYS 3.6 3.6 - - - +
3086 LEU* 1.3 77.9 - - - +
3106 ASP* 1.3 60.9 + - - +
3126 SER* 2.9 23.0 + - - -
3136 ILE* 3.6 18.2 + - + +
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Residues in contact with ASP 310 (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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593 ARG* 5.5 1.6 + - - -
3066 LYS* 2.8 59.5 + - - +
3076 ILE* 4.0 6.2 - - - +
3086 LEU 3.3 0.4 - - - -
3096 GLU* 1.3 78.8 - - - +
3116 ASN* 1.3 62.4 + - - +
3126 SER 3.2 0.2 - - - -
3136 ILE* 3.3 18.2 + - - +
3156 GLN* 3.0 30.2 + - + +
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Residues in contact with ASN 311 (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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3323 LEU* 3.5 40.6 - - + +
3353 LEU* 4.1 6.3 - - + +
3513 ALA* 4.9 8.7 + - - +
3573 PHE* 4.5 10.7 - - + -
2986 ALA* 4.0 10.2 - - - +
3076 ILE* 2.7 32.1 + - - +
3086 LEU 3.2 4.1 + - - +
3096 GLU 3.1 0.6 - - - -
3106 ASP* 1.3 82.6 - - - +
3126 SER* 1.3 62.1 + - - +
3136 ILE 3.4 4.1 - - - +
3156 GLN* 3.7 19.1 + - - +
3176 LYS* 5.1 5.9 + - - -
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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