Contacts of the strand formed by residues 165 - 172 (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 165 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1633 PRO* 3.8 2.0 - - - +
1643 ASP* 1.3 95.7 + - - +
1663 CYS* 1.3 62.8 + - - +
2243 GLU* 6.2 3.6 - - + -
2253 PHE 3.6 5.8 - - - +
2263 ASP* 3.5 26.9 - - + +
2273 LEU* 5.2 0.9 - - - -
2603 ILE* 3.6 4.0 - - - +
2613 VAL* 2.8 54.2 + - + +
2703 PRO* 6.4 0.4 - - - +
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Residues in contact with CYS 166 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333 TRP* 3.8 21.5 - - + -
1383 LEU* 3.6 27.4 - - + -
1443 MET* 4.6 0.2 - - - -
1633 PRO* 6.3 0.2 - - + -
1653 LYS* 1.3 77.1 - - - +
1673 SER* 1.3 61.9 + - - +
2243 GLU* 3.3 4.9 - - - +
2253 PHE* 2.9 56.6 + - - -
2273 LEU* 4.4 4.3 - - - -
2593 ASP 3.3 5.4 - - - +
2603 ILE* 3.6 23.1 - - + -
2613 VAL* 5.5 0.9 - - - -
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Residues in contact with SER 167 (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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1383 LEU* 4.8 1.5 - - - +
1663 CYS* 1.3 79.5 - - - +
1683 ILE* 1.3 62.1 + - - +
1693 HIS* 2.9 32.7 + - - -
2213 LYS* 4.8 4.7 - - - -
2233 ILE 3.2 11.9 - - - -
2243 GLU* 3.6 11.9 - - - -
2253 PHE* 5.6 0.2 - - - -
2583 PHE* 3.3 4.7 - - - -
2593 ASP* 2.9 38.1 + - - +
2613 VAL* 6.0 1.7 - - - +
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Residues in contact with ILE 168 (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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1373 PHE* 3.9 35.9 - - + +
1383 LEU* 3.6 32.5 - - + -
1393 LEU* 4.5 5.2 - - + -
1673 SER* 1.3 68.2 - - - +
1693 HIS* 1.3 73.2 + - - +
2213 LYS* 4.4 0.2 - - - -
2223 LEU* 3.3 39.8 + - + +
2233 ILE* 2.8 25.9 + - + +
2253 PHE* 4.2 6.9 - - + -
2373 PHE* 3.7 30.7 - - + -
2563 THR* 4.1 2.5 - - - +
2573 TRP 3.6 9.6 - - - +
2583 PHE* 4.4 0.9 - - + +
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Residues in contact with HIS 169 (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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1673 SER* 2.9 37.8 + - - -
1683 ILE* 1.3 93.0 + - - +
1703 LEU* 1.3 60.6 + - - +
2193 SER* 5.2 5.2 - - - -
2203 ASP 3.7 15.3 - - - +
2213 LYS* 4.0 20.1 - - + +
2223 LEU* 4.3 2.9 - - - -
2563 THR* 2.9 4.9 + - - -
2573 TRP* 2.7 73.4 + + + +
2593 ASP* 3.3 23.3 + - - -
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Residues in contact with LEU 170 (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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1693 HIS* 1.3 75.4 - - - +
1713 ALA* 1.3 63.9 + - - +
2193 SER* 3.4 4.5 - - - -
2203 ASP 3.1 40.9 + - - +
2223 LEU* 3.9 25.6 - - + -
2413 PHE* 4.0 38.4 - - + -
2433 LEU* 3.8 10.4 - - + +
2543 ILE* 3.5 40.8 - - + -
2553 VAL 3.3 11.2 - - - +
2563 THR* 3.7 10.5 - - - +
2573 TRP* 3.7 4.5 - - - -
3073 LEU* 5.2 4.7 - - + -
3233 ILE* 5.7 0.4 - - + -
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Residues in contact with ALA 171 (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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1703 LEU* 1.3 77.7 - - - +
1723 GLY* 1.3 61.2 + - - +
2153 VAL* 3.7 24.5 - - + -
2173 THR* 3.5 9.6 - - - +
2193 SER* 4.0 7.6 - - - +
2433 LEU* 4.2 3.6 - - - -
2543 ILE* 3.1 11.6 - - - +
2553 VAL* 2.8 33.3 + - + -
2573 TRP* 3.4 22.0 - - + -
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Residues in contact with GLY 172 (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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1713 ALA* 1.3 73.9 - - - +
1733 LEU* 1.3 59.4 + - - +
2153 VAL* 3.3 10.9 - - - +
2163 ASN* 2.8 35.3 + - - -
2173 THR* 2.6 27.2 + - - -
2433 LEU* 4.9 0.9 - - - -
2513 ILE* 4.3 7.0 - - - -
2533 GLY 3.9 4.3 - - - -
2543 ILE* 4.6 4.0 - - - -
2553 VAL* 4.3 1.1 - - - +
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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