Contacts of the helix formed by residues 315 - 327 (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 GLN 315 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513 ALA* 5.8 0.2 - - - +
2186 HIS* 5.6 2.0 - - - -
3106 ASP* 3.0 35.5 + - + +
3116 ASN* 3.7 22.5 + - - +
3136 ILE* 3.5 5.8 + - + -
3146 PRO* 1.3 75.9 - - - +
3166 VAL* 1.3 54.8 + - - +
3176 LYS* 3.4 37.2 - - + +
3186 ASP* 2.5 49.4 + - - +
3196 ILE* 3.2 11.4 + - - +
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Residues in contact with VAL 316 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2186 HIS* 3.4 38.0 - - + +
2216 GLU* 4.0 22.4 - - + +
2226 ALA* 4.2 10.3 - - - +
2256 VAL* 5.2 4.7 - - + -
3156 GLN* 1.3 70.5 - - - +
3176 LYS* 1.3 68.4 + - - +
3186 ASP 3.0 0.9 + - - -
3196 ILE* 3.9 9.4 - - - +
3206 ILE* 3.0 41.6 + - + +
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Residues in contact with LYS 317 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3116 ASN* 5.1 5.8 + - - -
3156 GLN* 3.1 34.2 - - + +
3166 VAL* 1.3 79.3 - - - +
3186 ASP* 1.3 74.3 + - - +
3206 ILE* 3.3 7.2 + - - +
3216 PHE* 2.9 26.6 + - - +
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Residues in contact with ASP 318 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3513 ALA* 3.0 31.3 - - + +
3523 ASN* 3.5 18.9 + - - +
3553 ILE* 3.9 14.4 - - - +
2956 VAL* 4.1 9.0 - - + +
3156 GLN* 2.5 41.0 + - - +
3176 LYS* 1.3 85.7 - - - +
3196 ILE* 1.3 59.0 + - - +
3206 ILE 3.1 1.3 - - - -
3216 PHE* 4.2 4.5 - - - +
3226 ALA* 2.9 30.7 + - - +
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Residues in contact with ILE 319 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2096 VAL* 4.8 2.7 - - + -
2156 PRO* 5.8 0.2 - - + -
2186 HIS* 3.8 36.3 - - + +
2196 CYS* 4.1 9.9 - - - -
2226 ALA* 4.1 16.2 - - + -
2606 VAL* 5.3 1.6 - - + -
2626 VAL* 3.7 44.4 - - + -
2956 VAL* 4.3 12.3 - - + -
3146 PRO* 4.9 4.5 - - + +
3156 GLN 3.2 13.0 + - - +
3166 VAL* 4.0 5.6 - - - +
3186 ASP* 1.3 78.0 - - - +
3206 ILE* 1.3 60.0 + - - +
3226 ALA* 4.1 0.9 - - - +
3236 ILE* 3.1 34.7 + - + +
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Residues in contact with ILE 320 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2226 ALA* 3.8 20.6 - - + +
2256 VAL* 3.7 32.8 - - + -
2266 LEU* 4.4 13.9 - - + +
3166 VAL* 3.0 34.7 + - + +
3176 LYS* 3.5 9.0 - - - +
3196 ILE* 1.3 76.4 - - - +
3216 PHE* 1.3 59.6 + - - +
3236 ILE* 3.1 7.2 + - - +
3246 LYS* 2.9 49.3 + - + +
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Residues in contact with PHE 321 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3523 ASN* 4.0 13.9 - - - +
3543 TRP* 3.7 31.6 - + + -
3553 ILE* 6.4 0.4 - - + -
3176 LYS 2.9 16.7 + - - +
3186 ASP* 3.3 8.9 + - - +
3206 ILE* 1.3 78.3 - - - +
3226 ALA* 1.3 62.8 + - - +
3246 LYS* 4.3 4.6 - - - +
3256 LYS* 3.2 52.2 + - + +
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Residues in contact with ALA 322 (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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3523 ASN* 4.5 2.5 - - - +
3543 TRP* 3.9 22.8 - - + -
2606 VAL* 4.5 4.9 - - + -
2936 VAL* 4.0 11.3 - - + +
2956 VAL* 3.5 25.8 - - + -
3186 ASP 2.9 17.7 + - - +
3196 ILE 4.1 2.7 - - - +
3216 PHE* 1.3 75.5 - - - +
3236 ILE* 1.3 66.7 + - - +
3256 LYS* 3.7 2.1 - - - +
3266 THR* 3.1 28.2 + - - -
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Residues in contact with ILE 323 (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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2076 ILE* 3.9 26.0 - - + -
2096 VAL* 3.7 27.4 - - + -
2226 ALA* 5.2 3.8 - - + -
2266 LEU* 3.6 33.9 - - + -
2316 VAL* 4.8 1.3 - - + -
2336 CYS* 4.2 4.0 - - - -
2606 VAL* 4.2 19.1 - - + -
3196 ILE* 3.1 28.7 + - + +
3206 ILE* 3.1 4.8 + - - +
3226 ALA* 1.3 75.7 - - - +
3246 LYS* 1.3 67.2 + - - +
3266 THR* 2.9 13.0 + - - -
3276 LEU* 3.1 21.5 + - + +
3296 ILE* 6.2 0.4 - - + -
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Residues in contact with LYS 324 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2266 LEU* 4.5 14.1 - - + +
2296 GLU* 3.0 32.8 + - - -
3206 ILE* 2.9 33.5 + - + +
3216 PHE* 4.3 4.9 - - - +
3236 ILE* 1.3 76.5 - - - +
3256 LYS* 1.3 63.2 + - - +
3276 LEU 3.3 0.2 + - - -
3286 ASN* 3.0 4.7 + - - -
3296 ILE* 3.0 69.7 + - + +
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Residues in contact with LYS 325 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3543 TRP* 3.0 56.0 - - + +
3216 PHE* 3.2 40.4 + - + +
3226 ALA 3.7 4.9 - - - +
3246 LYS* 1.3 78.0 - - - +
3266 THR* 1.3 62.3 + - - +
3286 ASN* 3.3 16.2 + - - +
3296 ILE 5.4 0.2 - - - -
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Residues in contact with THR 326 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3543 TRP* 5.2 0.4 - - - -
2076 ILE* 3.9 17.9 - - + -
2586 HIS* 3.7 25.8 + - + -
2596 LEU 4.8 3.4 - - - +
2606 VAL* 3.9 3.3 - - + +
2906 ALA* 3.7 26.1 - - + +
2916 PRO 4.2 7.5 + - - +
2936 VAL* 3.1 35.2 - - - +
3226 ALA 3.1 8.5 + - - -
3236 ILE 2.9 6.5 + - - -
3256 LYS* 1.3 74.9 - - - +
3276 LEU* 1.3 57.7 + - - +
3286 ASN* 3.0 8.7 + - - +
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Residues in contact with LEU 327 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2066 HIS* 3.5 25.8 - - + +
2076 ILE* 4.1 22.4 - - + -
2316 VAL* 4.1 19.7 - - + -
2586 HIS* 3.2 35.2 - - + +
3236 ILE* 3.1 17.5 + - + +
3266 THR* 1.3 75.0 - - - +
3286 ASN* 1.3 70.1 + - - +
3296 ILE* 3.1 38.6 + - + +
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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