Contacts of the strand formed by residues 219 - 230 (chain 2) 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 TRP 219 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352 TYR* 3.8 24.5 - + - -
812 LYS* 3.6 3.1 - - - +
822 LEU* 2.8 38.6 + - + +
1042 SER 5.4 1.8 + - - -
1062 TYR* 4.2 19.5 - + - -
1262 MET* 3.5 53.4 - - + -
1272 ILE 3.4 21.1 - - - -
1282 PRO* 3.7 15.5 - - + -
1862 PRO* 4.2 5.4 - - + -
2022 VAL* 3.6 25.5 - - + +
2032 PRO* 3.1 30.4 + - + -
2042 TYR* 4.8 1.7 - + - +
2052 VAL* 3.6 26.0 - - + +
2172 ASN* 4.7 2.3 - - - +
2182 ASN* 1.3 92.3 + - + +
2202 SER* 1.3 62.8 + - - +
2212 LEU 4.3 0.2 - - - -
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Residues in contact with SER 220 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1951 ASP* 3.7 2.8 + - - -
792 TRP* 6.0 1.6 - - - -
802 TRP 3.5 7.9 - - - -
812 LYS* 2.8 35.1 + - - +
822 LEU* 5.9 0.2 - - - -
1252 VAL 3.4 1.7 - - - +
1262 MET* 3.4 7.2 - - - -
1272 ILE* 2.8 33.4 + - - +
1302 HIS* 3.2 32.8 + - - +
2192 TRP* 1.3 75.1 + - - +
2212 LEU* 1.3 60.5 + - - +
2222 VAL* 3.7 4.3 + - - -
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Residues in contact with LEU 221 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792 TRP* 3.1 7.1 - - - +
802 TRP* 2.8 59.8 + - + +
822 LEU* 5.3 8.1 - - + +
1082 VAL* 3.9 16.2 - - + -
1102 VAL* 4.7 0.7 - - + -
1242 VAL* 3.8 26.2 - - + -
1252 VAL 3.4 13.0 - - - +
1262 MET* 4.0 20.2 - - + +
2202 SER* 1.3 71.8 - - - +
2222 VAL* 1.3 62.9 + - - +
2232 ILE* 4.3 7.2 - - + -
2422 VAL* 3.9 31.4 - - + -
2442 ILE* 4.7 7.9 - - + -
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Residues in contact with VAL 222 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 TRP 3.7 5.4 - - - +
792 TRP* 4.1 11.0 - - + -
1232 LEU 3.4 2.1 - - - +
1252 VAL* 2.9 41.5 + - + +
1272 ILE* 3.8 28.0 - - + -
1302 HIS* 4.1 16.6 - - + +
1742 PHE* 4.2 12.1 - - + -
1822 LEU* 4.9 9.9 - - + -
2202 SER* 4.4 5.6 - - - +
2212 LEU* 1.3 76.7 - - - +
2232 ILE* 1.3 68.8 + - - +
2242 ILE* 3.7 29.2 - - + -
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Residues in contact with ILE 223 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772 GLY* 3.2 4.0 - - - -
782 TRP* 2.9 58.5 + - + +
802 TRP* 3.8 26.5 - - + -
1102 VAL* 4.1 31.0 - - + -
1222 LEU* 4.1 28.9 - - + -
1232 LEU 3.3 3.6 - - - +
1242 VAL* 4.4 8.5 - - + -
2212 LEU* 4.3 12.3 - - + -
2222 VAL* 1.3 78.5 - - - +
2242 ILE* 1.3 63.7 + - - +
2402 ILE* 4.5 7.2 - - + -
2422 VAL* 4.3 6.5 - - + -
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Residues in contact with ILE 224 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 LYS 3.9 16.8 - - - +
772 GLY* 4.2 3.6 - - - -
782 TRP 4.8 1.1 - - - +
1222 LEU* 4.4 2.2 - - - -
1232 LEU* 2.9 41.6 + - + +
1702 ASN* 4.0 25.6 - - + +
1742 PHE* 4.2 10.5 - - + -
1792 LEU* 4.2 25.8 - - + -
1822 LEU* 5.1 2.2 - - + -
2222 VAL* 3.7 24.2 - - + -
2232 ILE* 1.3 83.6 - - - +
2252 PRO* 1.3 75.7 - - + +
2262 VAL* 3.0 9.0 + - + -
653 VAL* 4.3 10.8 - - + -
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Residues in contact with PRO 225 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.6 30.5 - - + +
752 SER* 3.5 26.2 - - - +
762 LYS* 3.8 4.7 - - - -
772 GLY* 3.7 21.5 - - - +
782 TRP* 4.2 9.6 - - + -
1212 THR 3.4 7.4 - - - +
1222 LEU* 3.8 11.6 - - + -
1702 ASN* 5.6 0.2 - - - +
2232 ILE 4.1 1.1 - - - +
2242 ILE* 1.3 86.3 - - + +
2262 VAL* 1.3 61.5 + - - +
2272 CYS 3.3 5.6 - - - +
2282 GLN* 5.0 2.7 + - - +
653 VAL* 4.1 10.9 - - - +
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Residues in contact with VAL 226 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212 THR* 2.8 32.4 + - + +
1232 LEU* 4.1 17.7 - - + +
1792 LEU* 4.5 15.9 - - + -
1892 PHE* 4.2 8.7 - - + -
2242 ILE* 3.0 19.9 + - + +
2252 PRO* 1.3 72.5 - - - +
2272 CYS* 1.3 57.5 + - - +
2282 GLN 4.1 0.8 + - - -
523 LEU* 5.1 8.7 - - + -
653 VAL* 4.2 20.3 - - + +
683 TYR* 6.2 3.4 - - + -
693 THR* 3.5 21.4 - - + +
2103 LEU* 4.0 22.9 - - + -
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Residues in contact with CYS 227 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712 TRP* 3.7 6.2 - - - -
1202 GLY* 3.3 4.1 - - - -
1212 THR* 2.9 40.8 + - - +
2252 PRO 4.7 1.6 - - - -
2262 VAL* 1.3 84.4 - - - +
2282 GLN* 1.3 67.7 + - - +
2292 LEU 3.5 0.7 + - - -
693 THR* 4.1 8.5 - - - -
1203 CYS* 3.6 30.5 - - + -
2083 GLU* 3.6 29.4 - - + -
2103 LEU* 4.3 8.5 - - - -
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Residues in contact with GLN 228 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 5.1 2.2 - - - +
732 SER* 3.2 45.5 + - - +
742 THR* 5.9 0.2 - - - +
1192 GLN* 3.5 8.5 - - - +
1202 GLY* 3.6 1.7 - - - -
2252 PRO* 5.0 4.6 + - - -
2262 VAL 4.1 1.2 + - - -
2272 CYS* 1.3 75.6 - - - +
2292 LEU* 1.3 72.3 + - - +
2302 GLN* 3.1 36.7 + - - +
2083 GLU* 5.2 6.5 - - + +
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Residues in contact with LEU 229 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.3 63.1 - - + +
722 ASN* 4.4 4.7 - - - -
732 SER* 4.1 17.9 + - - +
1182 HIS* 4.2 17.7 - - + -
1192 GLN 3.4 8.5 - - - +
1922 LEU* 3.6 29.6 - - + -
2272 CYS 3.5 1.4 + - - -
2282 GLN* 1.3 78.3 - - - +
2302 GLN* 1.3 68.0 + - - +
2382 VAL* 4.1 21.5 - - + +
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Residues in contact with GLN 230 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182 HIS* 3.4 4.1 - - - +
1192 GLN* 2.9 61.4 + - + +
2282 GLN* 3.1 40.9 + - - +
2292 LEU* 1.3 83.9 - - - +
2312 SER* 1.3 65.5 + - - +
2342 ILE* 6.0 1.3 - - - -
2043 PRO* 4.1 11.0 - - + +
2063 THR* 3.9 14.7 + - - +
2083 GLU* 4.8 12.9 + - - +
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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