Contacts of the strand formed by residues 99 - 111 (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 HIS 99 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542 THR* 3.6 19.5 - - + +
952 ASN* 2.9 47.2 + - - +
962 MET* 3.5 16.3 - - - +
972 PHE 3.2 0.2 - - - -
982 TYR* 1.3 91.1 - - + +
1002 PHE* 1.3 65.0 + - - +
1012 LEU 3.6 12.3 - - - +
2142 VAL* 5.9 0.7 - - - +
2512 PHE* 3.5 9.6 - - + +
2522 SER* 3.4 22.0 - - - +
2532 GLY 3.4 2.9 - - - -
2542 ALA* 3.5 36.7 - - + +
2552 ARG* 3.6 10.3 + - - -
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Residues in contact with PHE 100 (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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992 HIS* 1.3 75.0 - - - +
1012 LEU* 1.3 91.1 + - + +
2122 SER* 3.4 38.9 + - - -
2132 MET 4.3 2.3 + - - -
2152 ARG* 4.4 20.2 - - - -
2522 SER 4.3 1.3 - - - +
2532 GLY* 3.0 19.8 + - - +
2552 ARG* 3.5 23.6 - - - +
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Residues in contact with LEU 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482 THR* 6.1 2.0 - - + -
492 ALA* 3.7 29.8 - - + -
992 HIS* 3.6 5.8 - - - +
1002 PHE* 1.3 114.6 - - + +
1022 GLY* 1.3 58.5 + - - +
2102 MET* 4.1 23.6 - - + +
2112 ASP* 3.4 27.6 - - - +
2122 SER 4.3 0.2 - - - +
2132 MET* 5.1 1.1 - - - -
2512 PHE* 3.4 8.8 - - - +
2522 SER* 3.0 40.4 + - - +
2532 GLY* 5.8 0.7 - - - -
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Residues in contact with GLY 102 (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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1012 LEU* 1.3 77.4 - - - +
1032 ARG* 1.3 62.3 + - - +
2042 TYR* 4.3 4.5 + - - -
2102 MET* 3.8 3.8 - - - -
2112 ASP* 2.8 31.2 + - - +
2132 MET* 3.8 19.1 - - - +
2502 GLU 3.5 9.0 - - - -
2512 PHE* 3.8 11.9 - - - -
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Residues in contact with ARG 103 (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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402 HIS* 3.3 41.0 + - - -
422 LEU* 3.7 32.0 - - - +
1022 GLY* 1.3 75.4 - - - +
1042 SER* 1.3 68.3 + - - +
2042 TYR* 3.4 45.4 + - + +
2092 PRO* 3.0 31.1 + - - +
2102 MET* 4.0 10.1 - - + -
2132 MET* 4.1 4.4 - - - +
2482 CYS 3.6 3.4 + - - +
2492 ALA* 3.2 1.7 - - - +
2502 GLU* 2.9 62.0 + - + +
2512 PHE* 4.9 1.1 - - - -
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Residues in contact with SER 104 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922 PHE* 4.2 10.8 - - - -
1032 ARG* 1.3 82.7 - - - +
1052 GLY* 1.3 72.9 + - - +
1062 TYR* 3.8 18.8 + - - -
2032 PRO 4.8 0.2 - - - +
2042 TYR* 3.6 29.4 - - - +
2132 MET* 4.2 11.8 - - - +
2182 ASN* 6.0 0.2 + - - -
2192 TRP* 5.4 1.2 + - - -
2462 PRO* 3.6 17.7 - - - +
2472 MET 3.7 7.3 + - - -
2482 CYS 4.2 2.0 - - - -
2492 ALA* 4.0 12.4 - - - +
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Residues in contact with GLY 105 (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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392 PRO* 4.1 12.0 - - - +
1042 SER* 1.3 81.6 + - - +
1062 TYR* 1.3 70.4 + - - -
2022 VAL 3.3 13.7 - - - -
2032 PRO 4.3 5.8 - - - -
2042 TYR 4.4 0.7 - - - -
2472 MET* 2.7 36.0 + - - -
2482 CYS* 5.3 0.2 - - - +
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Residues in contact with TYR 106 (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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822 LEU* 3.9 31.0 - - + -
832 PRO* 3.5 28.6 - - + +
862 LEU* 3.9 20.4 - - + -
922 PHE* 4.2 4.2 - + - -
1042 SER* 3.8 26.8 + - - -
1052 GLY* 1.3 78.5 - - - -
1072 THR* 1.3 62.9 + - - +
1082 VAL* 4.0 7.6 - - + -
2002 LEU 3.8 0.5 - - - +
2012 ILE* 3.3 5.0 - - - +
2022 VAL* 2.8 51.4 + - + +
2132 MET* 4.1 12.1 - - - +
2182 ASN* 4.9 5.2 + - + -
2192 TRP* 4.2 14.1 - + - -
2442 ILE* 3.9 21.8 - - + -
2452 SER 3.2 7.2 - - - +
2462 PRO* 3.8 12.3 - - + -
2472 MET* 3.9 6.1 - - - +
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Residues in contact with THR 107 (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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162 ILE* 4.3 5.6 - - + -
182 ARG* 3.1 26.5 + - - +
632 PHE* 3.6 27.9 - - + -
1062 TYR* 1.3 72.7 - - - +
1082 VAL* 1.3 62.2 + - - +
1992 THR* 4.3 14.1 - - + -
2002 LEU 3.4 3.6 - - - -
2012 ILE* 3.7 12.5 - - + +
2432 SER 3.8 1.2 - - - +
2442 ILE* 3.4 5.4 - - - +
2452 SER* 2.9 32.6 + - - -
2472 MET* 3.0 24.8 - - - -
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Residues in contact with VAL 108 (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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822 LEU* 4.7 4.3 - - + -
1062 TYR* 4.3 13.5 - - + +
1072 THR* 1.3 78.1 - - - +
1092 HIS* 1.3 60.3 + - - +
1102 VAL* 4.3 13.2 - - + -
1262 MET* 3.9 28.7 - - + -
1982 ALA 3.5 1.9 - - - +
1992 THR* 3.3 5.0 - - - +
2002 LEU* 2.7 50.8 + - + +
2022 VAL* 5.2 0.4 - - + -
2212 LEU* 3.9 32.3 - - + -
2422 VAL* 4.5 1.6 - - + -
2432 SER 3.8 2.0 - - - -
2442 ILE* 4.3 16.4 - - + -
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Residues in contact with HIS 109 (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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142 ILE* 4.7 4.0 - - + -
162 ILE* 4.1 10.5 - - + +
232 ILE* 3.5 30.3 - - + +
242 THR 4.3 2.0 + - - -
252 SER* 4.2 13.8 - - - -
632 PHE* 4.2 16.6 - - + -
1072 THR 3.9 0.4 + - - -
1082 VAL* 1.3 74.0 - - - +
1102 VAL* 1.3 59.7 + - - +
1112 GLN* 3.0 50.1 + - + +
1972 SER* 3.6 32.1 - - - -
1982 ALA 3.3 1.8 + - - -
1992 THR* 2.8 28.8 + - + +
2432 SER* 2.9 29.1 + - - +
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Residues in contact with VAL 110 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082 VAL* 4.3 15.7 - - + -
1092 HIS* 1.3 74.1 - - - +
1112 GLN* 1.3 64.6 + - - +
1222 LEU* 5.3 2.5 - - + -
1242 VAL* 3.9 28.5 - - + -
1902 ILE* 3.7 20.1 - - + +
1972 SER* 3.1 9.0 - - - -
1982 ALA* 2.9 37.2 + - + +
2002 LEU* 5.5 0.2 - - + -
2212 LEU* 4.7 1.8 - - + -
2232 ILE* 4.1 17.0 - - + -
2402 ILE* 4.0 24.0 - - + -
2412 THR 3.6 3.8 - - - +
2422 VAL* 4.4 9.0 - - + +
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Residues in contact with GLN 111 (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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232 ILE* 5.3 4.1 - - - +
242 THR 6.0 0.4 - - - +
1092 HIS* 3.0 50.6 + - + +
1102 VAL* 1.3 74.3 - - - +
1122 CYS* 1.3 65.5 + - - +
1132 ASN* 5.6 1.3 - - - +
1902 ILE* 4.9 0.2 - - - -
1962 ASN 3.9 4.7 - - - +
1972 SER* 4.9 1.3 - - - -
2392 PRO 4.1 0.5 - - - +
2402 ILE* 3.4 4.2 - - - +
2412 THR* 2.7 60.7 + - - +
2432 SER* 3.0 27.6 + - - +
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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