Contacts of the helix formed by residues 305 - 310 (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 305 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3044 TYR* 1.3 80.2 - - - +
3064 LYS* 1.3 55.5 + - - +
3074 ILE 3.2 1.8 - - - +
3084 LEU* 2.9 27.4 + - + +
3094 GLU 2.7 31.7 + - - -
595 ARG* 4.4 0.2 - - - +
1115 GLY* 3.9 17.9 - - - +
1195 GLY 2.9 22.3 + - - +
3295 GLU* 4.6 1.1 - - - +
3305 PRO* 3.9 16.6 - - + -
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Residues in contact with LYS 306 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3054 ALA* 1.3 67.5 - - - +
3074 ILE* 1.3 69.4 + - - +
3094 GLU* 4.4 1.6 - - - +
3104 ASP* 2.9 64.5 + - - +
595 ARG* 3.2 47.7 - - - +
1115 GLY 5.4 0.2 + - - -
3295 GLU* 3.5 11.6 + - - +
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Residues in contact with ILE 307 (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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3054 ALA* 5.0 0.2 - - + -
3064 LYS* 1.3 79.5 - - - +
3084 LEU* 1.3 80.5 + - + +
3104 ASP* 3.6 4.1 + - + -
3114 ASN* 2.9 42.4 + - - +
3295 GLU* 2.9 31.6 + - + +
3305 PRO* 3.8 24.0 - - + +
3325 LEU* 4.3 22.2 - - + +
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Residues in contact with LEU 308 (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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3034 PRO* 3.6 19.5 - - + -
3054 ALA* 2.9 17.1 + - + +
3074 ILE* 1.3 92.0 - - + +
3094 GLU* 1.3 61.8 + - - +
3114 ASN 3.2 6.4 + - - -
3124 SER* 2.9 19.2 + - - -
1185 LYS 4.8 0.7 - - - +
1195 GLY 4.7 1.8 - - - +
1205 LYS* 4.1 30.1 - - + -
3305 PRO* 3.5 25.8 - - + -
3315 PRO 4.0 15.5 - - - +
3325 LEU* 4.1 7.6 - - + -
3345 GLU 5.6 0.4 - - - -
3355 LEU* 3.4 35.1 - - + +
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Residues in contact with GLU 309 (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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1214 SER 3.8 13.2 + - - +
1224 ALA* 3.8 10.9 + - - -
1234 GLY* 3.1 33.2 + - - -
1244 VAL 4.6 2.3 + - - -
1254 ALA 5.5 0.2 + - - -
1294 SER* 4.8 0.7 + - - -
3024 MET* 3.9 23.3 - - - +
3034 PRO* 3.9 17.6 - - - +
3044 TYR 4.2 2.5 - - - +
3054 ALA 2.7 18.4 + - - +
3064 LYS 4.0 2.2 - - - +
3084 LEU* 1.3 69.4 - - - +
3104 ASP* 1.3 59.7 + - - +
3114 ASN 2.7 15.2 + - - -
3124 SER* 2.8 20.9 + - - -
3134 ILE* 3.6 18.1 + - + +
595 ARG* 3.3 19.1 + - - +
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Residues in contact with ASP 310 (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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3064 LYS* 2.9 59.1 + - - +
3074 ILE* 4.1 5.2 - - + +
3094 GLU* 1.3 79.2 - - - +
3114 ASN* 1.3 62.8 + - - +
3124 SER 3.4 0.9 - - - -
3134 ILE* 3.9 4.6 - - - +
3154 GLN* 3.0 43.1 + - - +
595 ARG* 5.1 0.3 + - - -
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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