Contacts of the helix formed by residues 305 - 321 (chain 9) in PDB entry 6FF7
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 PRO 305 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1979 THR* 5.8 7.4 - - - -
3019 PHE 3.1 15.2 - - - +
3029 ALA* 3.1 9.1 - - - +
3039 LYS 3.0 1.0 - - - -
3049 ASN* 1.3 78.8 - - - +
3069 LYS* 1.3 64.6 + - - -
3079 SER 3.1 3.4 - - - -
3089 LYS* 2.8 25.5 + - + +
3099 GLY* 2.9 10.6 + - - +
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Residues in contact with LYS 306 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1719 PHE* 6.3 2.7 - - + -
3029 ALA 3.1 8.8 + - - +
3039 LYS* 3.2 15.8 + - - +
3049 ASN 3.5 1.4 + - - -
3059 PRO* 1.3 76.0 - - - +
3079 SER* 1.3 58.1 + - - +
3099 GLY* 3.3 2.7 + - - +
3109 THR* 2.9 30.5 + - - -
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Residues in contact with SER 307 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3049 ASN 5.4 0.4 + - - -
3059 PRO 3.0 1.7 + - - -
3069 LYS* 1.3 78.9 - - - +
3089 LYS* 1.3 56.9 + - - +
3109 THR* 3.6 5.5 + - - -
3119 LYS* 2.9 28.8 + - - +
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Residues in contact with LYS 308 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379 GLY 4.7 9.4 - - - +
1389 ARG 4.5 11.8 - - - +
1399 TYR* 5.0 1.4 - - - -
1409 LEU* 5.1 10.7 + - + +
3059 PRO* 2.8 18.2 + - + +
3079 SER* 1.3 75.8 - - - +
3099 GLY* 1.3 67.0 + - - +
3119 LYS* 3.3 7.2 + - - +
3129 ARG* 2.9 26.3 + - - +
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Residues in contact with GLY 309 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409 LEU* 6.5 0.4 - - - -
3059 PRO* 2.9 12.1 + - - +
3069 LYS* 3.7 3.8 - - - -
3089 LYS* 1.3 78.1 - - - +
3109 THR* 1.3 60.6 + - - +
3129 ARG* 3.2 4.8 + - - +
3139 ASP* 2.9 24.5 + - - +
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Residues in contact with THR 310 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3069 LYS 2.9 16.7 + - - -
3079 SER* 3.8 6.3 - - - -
3099 GLY* 1.3 73.1 - - - +
3119 LYS* 1.3 65.0 + - - +
3139 ASP* 3.2 7.2 + - - +
3149 THR* 2.9 25.2 + - - -
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Residues in contact with LYS 311 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1389 ARG 4.0 16.4 - - - +
1399 TYR* 5.8 0.2 - - - -
3079 SER 2.9 20.1 + - - +
3089 LYS* 3.3 6.7 + - - +
3109 THR* 1.3 77.0 - - - +
3129 ARG* 1.3 57.5 + - - +
3149 THR* 3.3 8.1 - - - -
3159 GLU* 3.0 24.8 + - - +
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Residues in contact with ARG 312 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1389 ARG 5.0 0.6 + - - -
1399 TYR* 4.3 8.7 - - + -
1409 LEU* 4.2 29.4 - - + +
3089 LYS 2.9 17.1 + - - +
3099 GLY* 3.7 5.2 - - - +
3119 LYS* 1.3 73.0 - - - +
3139 ASP* 1.3 67.1 + - - +
3159 GLU* 2.7 20.2 + - - +
3169 ARG* 2.8 13.9 + - - +
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Residues in contact with ASP 313 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649 LEU* 5.2 15.7 - - + -
3099 GLY 2.9 16.7 + - - +
3109 THR* 3.7 7.4 - - - +
3129 ARG* 1.3 75.7 - - - +
3149 THR* 1.3 63.7 + - - +
3169 ARG* 3.2 9.5 + - - +
3179 ASN* 3.0 22.5 + - - +
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Residues in contact with THR 314 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3109 THR 2.9 13.2 + - - -
3119 LYS* 3.3 12.6 - - - -
3139 ASP* 1.3 75.6 - - - +
3159 GLU* 1.3 64.0 + - - +
3179 ASN* 3.0 8.6 + - - +
3189 LYS* 2.9 22.4 + - - +
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Residues in contact with GLU 315 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1399 TYR* 5.5 0.4 - - + -
3119 LYS 3.0 12.5 + - - +
3129 ARG* 2.7 19.0 + - - +
3149 THR* 1.3 70.0 - - - +
3169 ARG* 1.3 64.6 + - - +
3189 LYS* 3.1 8.4 + - - +
3199 ASP* 2.9 26.0 + - - +
93h ASP* 6.0 3.4 - - + -
94h ARG* 5.8 3.1 - - - +
95h TYR* 5.0 20.0 - - + +
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Residues in contact with ARG 316 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1609 TYR* 6.1 5.6 - - + -
1619 ILE* 6.4 3.1 - - + -
3129 ARG 2.8 13.3 + - - +
3139 ASP* 3.3 13.2 - - - +
3159 GLU* 1.3 73.0 - - - +
3179 ASN* 1.3 62.7 + - - +
3199 ASP* 3.4 4.5 + - - +
3209 ILE* 2.9 25.7 + - - +
93h ASP* 6.1 3.1 - - - -
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Residues in contact with ASN 317 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3139 ASP 3.0 12.4 + - - +
3149 THR* 3.6 9.6 - - - +
3169 ARG* 1.3 76.2 - - - +
3189 LYS* 1.3 63.2 + - - +
3209 ILE* 3.3 8.3 + - - +
3219 ALA* 3.0 24.8 + - - +
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Residues in contact with LYS 318 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3149 THR 2.9 12.0 + - - +
3159 GLU* 3.3 11.7 - - - +
3179 ASN* 1.3 72.8 - - - +
3199 ASP* 1.3 59.0 + - - +
3219 ALA* 2.7 29.0 + - - +
3229 PHE* 3.1 9.6 + - - +
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Residues in contact with ASP 319 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3159 GLU 2.9 14.0 + - - +
3169 ARG* 3.9 3.8 - - - +
3189 LYS* 1.3 75.8 - - - +
3209 ILE* 1.3 62.7 + - - +
3229 PHE* 3.1 25.6 + - - +
3279 ILE* 4.9 8.6 - - + +
3309 TYR* 6.5 1.3 - - + -
73h MET* 6.2 0.4 - - + -
92h LYS 5.3 1.3 - - - -
93h ASP* 3.3 34.5 - - + +
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Residues in contact with ILE 320 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3169 ARG 2.9 20.3 + - - +
3179 ASN* 3.4 9.4 - - - +
3199 ASP* 1.3 77.7 - - - +
3219 ALA* 1.3 59.5 + - - +
3229 PHE 3.2 7.7 + - - +
91h ASN* 6.2 3.6 - - - -
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Residues in contact with ALA 321 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3179 ASN 3.0 13.8 + - - +
3189 LYS* 2.7 15.6 + - - +
3209 ILE* 1.3 69.5 - - - +
3229 PHE* 1.3 62.5 + - - +
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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