Contacts of the strand formed by residues 167 - 171 (chain 1) in PDB entry 1QJX
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 SER 167 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411 GLN* 3.2 18.2 + - - -
1421 TYR 3.3 7.2 - - - -
1431 MET* 3.2 21.3 - - - +
1621 SER* 2.6 26.6 + - - -
1651 ASN 3.6 2.0 + - - -
1661 ALA* 1.3 71.7 - - - +
1681 VAL* 1.3 66.9 + - - +
1691 PHE* 3.9 18.6 + - - -
70021 W02 4.3 0.2 - - - -
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Residues in contact with VAL 168 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 MET* 5.7 0.7 - - - -
1411 GLN* 3.5 2.6 - - - -
1421 TYR* 2.8 47.2 + - + +
1671 SER* 1.3 78.3 - - - +
1691 PHE* 1.3 71.1 + - - +
1771 PRO* 4.0 27.4 - - + -
1781 ARG 5.7 0.2 - - - +
1791 PHE* 3.9 26.5 - - + -
70021 W02 3.9 20.2 - - + +
243 ALA* 6.2 0.9 - - + -
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Residues in contact with PHE 169 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391 VAL* 4.8 9.9 - - + -
1401 MET 3.2 7.4 - - - +
1411 GLN* 3.5 47.6 - - + -
1601 TRP 5.2 1.8 - - - -
1621 SER* 5.8 2.5 - - - -
1671 SER* 3.9 20.2 - - - -
1681 VAL* 1.3 81.8 - - - +
1701 TRP* 1.3 60.4 + - - +
1711 GLN 4.3 0.3 + - - -
2201 ARG* 5.2 2.2 - - - -
2221 VAL* 4.0 16.2 - - + -
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Residues in contact with TRP 170 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261 PRO* 3.8 46.9 - - + -
1281 VAL* 4.8 8.7 - - + -
1381 ILE* 4.7 6.3 - - + -
1391 VAL* 3.3 7.0 - - - +
1401 MET* 2.8 52.3 + - + +
1421 TYR* 4.4 12.1 - - + -
1681 VAL 4.0 0.8 + - - -
1691 PHE* 1.3 75.0 - - - +
1711 GLN* 1.3 68.0 + - - +
1721 HIS* 3.3 37.2 - + + -
1731 GLY 3.9 3.1 - - - -
1741 GLN* 3.0 27.9 + - + -
1751 PRO 3.3 17.2 + - - -
1761 PHE* 4.5 3.7 - + - +
1771 PRO* 3.5 29.7 - - + +
2321 VAL* 6.1 0.2 - - + -
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Residues in contact with GLN 171 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 HIS* 3.1 34.7 + - - +
1381 ILE 3.8 2.5 - - - -
1391 VAL* 4.3 10.3 - - + +
1691 PHE 4.3 0.2 + - - -
1701 TRP* 1.3 82.9 - - - +
1721 HIS* 1.3 74.6 + - - +
1731 GLY 3.2 0.2 + - - -
1741 GLN* 3.0 42.8 + - + +
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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