Contacts of the strand formed by residues 139 - 145 (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 VAL 139 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 HIS* 3.5 32.5 - - + +
1381 ILE* 1.3 79.6 - - - +
1401 MET* 1.3 60.3 + - - +
1691 PHE* 4.8 10.3 - - + -
1701 TRP 3.3 13.2 - - - +
1711 GLN* 4.3 9.6 - - + -
2211 ILE* 3.6 4.9 - - - +
2221 VAL* 2.8 53.7 + - + +
2231 THR* 3.2 13.0 + - - +
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Residues in contact with MET 140 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821 LEU* 3.8 26.7 - - + -
1261 PRO* 5.2 0.2 - - + -
1381 ILE* 4.1 16.4 - - + -
1391 VAL* 1.3 75.4 - - - +
1411 GLN* 1.3 60.9 + - - +
1421 TYR* 3.6 44.6 - - + +
1681 VAL 3.7 0.4 - - - +
1691 PHE* 3.2 9.0 - - - +
1701 TRP* 2.8 53.1 + - + +
2191 SER* 4.7 1.6 - - - -
2201 ARG 3.7 13.5 - - - +
2211 ILE* 3.8 23.8 - - - -
2221 VAL* 4.0 2.2 - - - -
2321 VAL* 4.1 18.8 - - + -
2341 THR* 4.5 2.2 - - - +
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Residues in contact with GLN 141 (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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1401 MET* 1.3 74.9 - - - +
1421 TYR* 1.3 64.3 + - - +
1431 MET* 4.3 1.6 - - - +
1601 TRP* 3.2 40.6 + - + +
1621 SER* 4.3 0.8 - - - -
1671 SER* 3.2 26.9 + - - +
1681 VAL 3.5 4.0 - - - +
1691 PHE* 3.5 34.5 - - + -
2181 CYS 3.6 1.0 - - - +
2191 SER* 3.3 7.3 - - - -
2201 ARG* 2.8 70.3 + - + +
2221 VAL* 3.6 8.0 - - + +
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Residues in contact with TYR 142 (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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801 SER* 6.0 0.4 - - - -
1241 MET* 3.9 38.1 - - + -
1261 PRO* 3.7 10.3 - - + +
1401 MET* 3.6 37.8 - - + +
1411 GLN* 1.3 72.3 - - - +
1431 MET* 1.3 60.3 + - - +
1671 SER* 3.3 2.4 - - - -
1681 VAL* 2.8 52.6 + - + +
1701 TRP* 4.4 13.2 - - + -
1771 PRO* 4.9 4.3 - - + -
2171 LEU* 4.3 9.2 - - + -
2181 CYS 3.6 3.8 - - - -
2191 SER* 3.9 26.2 - - - -
2341 THR* 2.8 44.8 + - + +
2361 ILE* 5.4 0.7 - - + -
70021 W02 3.9 10.7 - - - +
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Residues in contact with MET 143 (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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1411 GLN* 3.9 2.9 - - - +
1421 TYR* 1.3 72.0 - - - +
1441 TYR* 1.3 73.1 + - - +
1451 VAL* 3.6 20.2 + - + -
1501 PRO 5.2 0.4 - - - +
1521 PRO* 4.2 15.5 - - + -
1591 ALA* 3.3 36.1 - - + +
1601 TRP* 4.0 24.0 - - + -
1621 SER* 3.6 18.4 - - - -
1651 ASN* 4.0 15.7 - - + +
1661 ALA 3.6 0.4 - - - -
1671 SER* 3.2 17.5 - - - +
2171 LEU* 3.6 5.8 - - - +
2181 CYS* 2.8 42.1 + - + +
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Residues in contact with TYR 144 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981 ILE* 3.6 14.1 - - + -
1431 MET* 1.3 71.4 - - - +
1451 VAL* 1.3 69.4 + - - +
1461 PRO* 3.3 39.2 - - + +
1471 PRO* 4.4 2.1 - - - +
1651 ASN* 3.3 18.5 - - - +
1661 ALA* 2.9 16.7 + - + +
1811 LEU* 5.4 2.5 - - + -
1841 LEU* 5.0 7.3 - - + +
2141 MET* 2.7 32.4 + - - +
2161 THR 3.7 7.0 - - - -
2171 LEU* 4.7 2.0 - - - -
70021 W02 3.2 59.0 - + + +
243 ALA* 6.6 0.4 - - + -
253 LEU* 4.8 26.7 - - + -
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Residues in contact with VAL 145 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431 MET* 3.9 26.5 - - + +
1441 TYR* 1.3 77.7 - - - +
1461 PRO* 1.3 65.1 - - - +
1471 PRO* 4.6 0.2 - - - +
1491 ALA* 3.5 39.0 - - + +
1501 PRO 4.1 9.0 - - - +
1511 ILE* 4.2 11.4 - - + -
1521 PRO* 4.6 0.4 - - + -
1651 ASN* 4.0 4.3 - - - +
2151 GLY* 3.6 0.2 - - - -
2161 THR* 2.8 45.1 + - - +
2181 CYS* 3.9 23.8 - - - -
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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
------------------------------------------------------------
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