Contacts of the strand formed by residues 340 - 347 (chain 3) in PDB entry 1G6Q
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 LYS 340 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2933 ASP* 6.1 0.2 - - - -
3253 TYR* 3.4 11.0 - - - +
3263 LYS* 4.2 22.0 - - + -
3383 SER 5.5 1.6 - - - +
3393 ARG* 1.3 78.9 - - - +
3413 ASN* 1.3 65.9 + - - +
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Residues in contact with ASN 341 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2923 PRO* 3.2 14.8 - - - +
2933 ASP* 3.2 29.4 - - - +
3243 SER* 4.9 0.2 - - - -
3253 TYR* 2.8 60.3 + - + -
3403 LYS* 1.3 75.2 - - - +
3423 GLU* 1.3 89.7 + - - +
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Residues in contact with GLU 342 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2923 PRO* 4.1 6.9 - - - +
3223 LYS* 3.4 27.6 - - - +
3233 ILE 3.2 7.2 - - - -
3243 SER* 5.0 5.8 + - - +
3253 TYR* 5.2 2.0 - - - -
3413 ASN* 1.3 94.7 + - - +
3433 GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 343 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2033 HIS* 5.6 4.9 - - - -
2923 PRO* 5.7 1.8 - - - -
3223 LYS* 3.0 8.9 - - - +
3233 ILE 2.7 38.8 + - - -
3253 TYR* 6.2 0.2 - - - -
3423 GLU* 1.3 76.9 - - - +
3443 SER* 1.3 61.4 + - - -
3453 TYR* 3.5 25.1 - - - -
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Residues in contact with SER 344 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2033 HIS* 4.0 20.5 + - - +
3213 ILE 3.6 6.5 - - - -
3223 LYS* 4.1 13.0 - - - +
3433 GLY* 1.3 72.7 - - - -
3453 TYR* 1.3 59.8 + - - +
3463 LEU 4.3 0.5 + - - -
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Residues in contact with TYR 345 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2023 LEU 3.6 11.2 - - - -
2033 HIS* 3.3 37.6 - + + +
2053 PRO* 4.1 11.0 - - + -
2893 PHE* 3.8 36.8 + + + +
2903 TYR 2.9 35.5 + - - -
2913 PHE* 4.4 8.8 - - - -
2923 PRO* 4.6 4.9 - - - +
3193 LEU 3.8 0.7 - - - +
3203 ASN* 4.0 1.4 - - - -
3213 ILE* 2.8 45.1 + - + +
3233 ILE* 3.9 28.8 - - + +
3253 TYR* 5.6 1.0 - - - -
3433 GLY* 3.5 30.0 - - - -
3443 SER* 1.3 73.1 - - - +
3463 LEU* 1.3 59.4 + - - +
3473 MET 3.9 0.6 + - - -
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Residues in contact with LEU 346 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2033 HIS 3.6 5.5 + - - -
2043 GLU* 3.3 18.5 - - - +
2053 PRO* 3.4 7.5 - - - +
3123 ASN* 4.0 14.6 - - - +
3183 ASP* 4.1 15.5 - - + +
3193 LEU 3.7 9.0 - - - +
3203 ASN* 3.8 18.2 - - - +
3443 SER 4.3 1.0 + - - -
3453 TYR* 1.3 72.3 - - - +
3473 MET* 1.3 76.9 - - - +
3483 HIS* 3.6 16.7 + - + -
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Residues in contact with MET 347 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363 TYR* 5.3 2.2 - - - -
1373 PHE* 3.6 39.0 - - + -
1403 TYR* 3.9 35.0 - - + -
2043 GLU* 4.4 1.6 - - - +
2053 PRO* 3.8 18.7 - - + +
2073 VAL* 6.0 4.5 - - + -
2873 THR* 4.4 8.3 - - + -
2893 PHE* 3.8 19.7 - - + -
3183 ASP* 3.6 12.5 - - - +
3193 LEU* 3.0 36.7 + - + +
3213 ILE* 3.7 26.9 - - + -
3453 TYR 3.9 1.0 + - - -
3463 LEU* 1.3 73.2 - - - +
3483 HIS* 1.3 60.4 + - - +
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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