Contacts of the strand formed by residues 238 - 254 (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 VAL 238 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712 TRP* 3.0 42.9 + - + +
1122 CYS* 3.9 21.1 - - - -
1132 ASN 3.8 21.5 - - - +
1142 ALA* 4.6 9.9 - - + -
1182 HIS* 4.2 26.5 - - + +
1922 LEU* 5.4 0.2 - - + -
2292 LEU* 4.1 19.0 - - + +
2362 ASN* 3.5 12.0 + - + +
2372 ILE* 1.3 78.8 - - - +
2392 PRO* 1.3 59.4 - - - +
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Residues in contact with PRO 239 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682 SER* 4.6 14.4 - - - -
692 LYS 3.0 15.7 - - - +
702 MET* 4.3 3.6 - - + -
1112 GLN 4.1 0.5 - - - +
1122 CYS* 3.7 22.7 - - - -
1132 ASN* 4.9 6.9 + - - +
2372 ILE* 3.4 20.2 - - + +
2382 VAL* 1.3 87.9 - - + +
2402 ILE* 1.3 63.7 + - - +
2412 THR* 4.2 3.1 - - - +
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Residues in contact with ILE 240 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672 ASP 4.7 0.3 - - - +
682 SER* 3.4 3.6 - - - -
692 LYS* 2.8 38.9 + - + +
712 TRP* 3.9 13.2 - - + -
782 TRP* 3.5 44.9 - - + -
802 TRP* 5.5 3.5 - - + -
1102 VAL* 4.0 20.0 - - + -
1112 GLN 3.4 9.4 - - - +
1122 CYS* 4.2 15.3 - - - -
1222 LEU* 3.9 18.6 - - + -
2232 ILE* 4.5 12.8 - - + -
2392 PRO* 1.3 78.1 - - - +
2412 THR* 1.3 67.5 + - - +
2422 VAL* 4.7 4.8 - - + +
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Residues in contact with THR 241 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 THR* 3.5 29.4 - - + -
662 LEU 4.4 2.2 - - - +
682 SER* 2.9 27.6 + - - +
1102 VAL* 3.6 1.9 - - - +
1112 GLN* 2.7 63.6 + - - +
2392 PRO* 4.2 4.0 - - - +
2402 ILE* 1.3 75.9 + - - +
2422 VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 242 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 TYR 3.9 0.3 - - - +
652 THR* 3.4 3.5 - - - +
662 LEU* 2.9 46.9 + - + +
672 ASP 5.2 2.6 + - - +
802 TRP* 4.0 30.7 - - + -
1082 VAL* 4.5 4.3 - - + -
1092 HIS 3.7 4.7 - - - +
1102 VAL* 4.4 7.6 - - + -
2212 LEU* 3.9 16.6 - - + -
2232 ILE* 4.3 13.9 - - + -
2402 ILE* 4.7 3.8 - - + +
2412 THR* 1.3 80.0 - - - +
2432 SER* 1.3 65.4 + - - +
2442 ILE* 3.8 27.1 - - + -
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Residues in contact with SER 243 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 ILE* 3.7 25.8 - - - +
632 PHE* 3.9 6.9 - - - -
642 TYR 3.3 6.5 - - - -
652 THR* 2.8 24.7 + - - +
1072 THR 3.8 1.0 - - - +
1092 HIS* 2.9 34.5 + - - +
1112 GLN* 3.0 24.0 + - - -
2422 VAL* 1.3 72.9 - - - +
2442 ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 244 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 ARG 3.6 1.9 - - - +
632 PHE* 3.9 1.1 - - - -
642 TYR* 2.8 42.1 + - - +
662 LEU* 3.9 26.2 - - + -
802 TRP* 5.8 1.8 - - + -
822 LEU* 3.7 27.8 - - + -
852 ALA* 5.1 0.9 - - + -
862 LEU* 4.1 17.5 - - + -
1062 TYR* 3.9 31.0 - - + -
1072 THR 3.4 8.1 - - - +
1082 VAL* 4.3 12.3 - - + -
2212 LEU* 4.7 9.4 - - + -
2422 VAL* 3.8 14.4 - - + -
2432 SER* 1.3 79.0 - - - +
2452 SER* 1.3 62.7 + - - +
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Residues in contact with SER 245 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 ARG* 3.5 23.1 - - - +
622 ARG 3.2 23.8 + - - -
632 PHE* 3.6 22.2 - - - -
1062 TYR* 3.2 2.3 - - - -
1072 THR* 2.9 38.0 + - - -
2442 ILE* 1.3 75.6 - - - +
2462 PRO* 1.3 77.9 + - - +
2472 MET* 3.8 1.4 - - - +
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Residues in contact with PRO 246 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 ARG* 5.0 0.3 - - - -
602 SER 3.3 20.6 - - - +
612 ASN* 3.3 20.7 - - - +
622 ARG 3.2 14.4 - - - +
642 TYR* 3.9 6.5 - - + -
862 LEU* 4.0 13.2 - - + -
922 PHE* 3.5 33.7 - - + -
1042 SER* 3.6 13.7 - - - +
1052 GLY 3.3 7.9 - - - +
1062 TYR* 3.8 4.7 - - + -
2442 ILE 3.9 3.6 - - - +
2452 SER* 1.3 96.9 + - - +
2472 MET* 1.3 61.0 + - - +
2492 ALA* 4.4 0.4 - - + -
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Residues in contact with MET 247 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 ARG* 3.9 22.9 - - - +
382 TRP* 3.7 31.6 - - + +
392 PRO* 3.6 34.4 - - + +
612 ASN* 4.1 3.8 - - + -
1042 SER* 3.7 0.4 + - - -
1052 GLY* 2.7 34.5 + - - +
1062 TYR 3.9 12.3 - - - +
1072 THR* 3.0 22.2 - - - +
2012 ILE* 4.1 2.9 - - - -
2452 SER 3.8 6.5 - - - +
2462 PRO* 1.3 82.0 - - - +
2482 CYS* 1.3 75.7 + - + +
2492 ALA 3.2 1.2 + - - -
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Residues in contact with CYS 248 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392 PRO* 3.8 25.4 - - + -
402 HIS* 3.8 23.5 - - - +
412 TYR* 3.6 46.3 - - + -
612 ASN* 3.6 9.5 - - - +
1032 ARG* 3.6 7.1 + - - +
1042 SER* 4.2 2.1 - - - -
1052 GLY 5.3 0.2 - - - +
2472 MET* 1.3 77.1 - - - +
2492 ALA* 1.3 63.9 + - - +
2502 GLU* 3.4 6.6 + - - +
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Residues in contact with ALA 249 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412 TYR* 3.9 4.5 + - - -
552 GLN* 3.8 5.4 - - - +
562 PRO* 3.7 15.4 - - - +
602 SER* 3.9 10.5 + - - +
612 ASN* 3.3 22.0 + - - +
922 PHE* 4.0 26.9 - - + -
1032 ARG 3.2 7.6 - - - +
1042 SER* 4.0 7.9 - - - +
2462 PRO* 4.4 0.9 - - + -
2472 MET 3.2 1.4 - - - -
2482 CYS* 1.3 77.5 - - - +
2502 GLU* 1.3 60.6 + - - +
2512 PHE* 4.1 10.3 - - + -
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Residues in contact with GLU 250 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412 TYR* 3.4 16.0 - - + +
422 LEU* 2.8 40.1 + - - +
532 PRO* 3.8 19.4 - - + +
542 THR 3.2 11.4 - - - +
552 GLN* 3.3 23.8 - - + +
1022 GLY* 3.5 0.5 - - - -
1032 ARG* 2.9 50.4 + - + -
2102 MET* 3.6 9.4 - - + +
2482 CYS 4.0 4.1 - - - +
2492 ALA* 1.3 75.6 - - - +
2512 PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 251 (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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522 LYS 4.7 0.2 - - - +
532 PRO* 3.2 4.7 - - - +
542 THR* 2.8 42.7 + - + +
562 PRO* 4.0 14.8 - - + -
602 SER* 5.1 1.1 - - - -
922 PHE* 4.0 28.5 - + - -
952 ASN* 3.5 42.2 - - + -
962 MET* 3.9 15.0 - - + -
992 HIS* 3.5 20.6 - - + +
1012 LEU 3.4 7.6 - - - +
1022 GLY* 3.8 10.8 - - - -
1032 ARG 5.0 0.7 - - - -
2102 MET* 4.2 2.9 - - - -
2132 MET* 3.8 24.2 - - + -
2492 ALA* 4.1 14.6 - - + -
2502 GLU* 1.3 85.5 - - - +
2522 SER* 1.3 62.5 + - - +
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Residues in contact with SER 252 (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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492 ALA* 3.9 11.4 - - - +
512 ASP* 2.5 35.4 + - - -
522 LYS 5.2 0.2 - - - -
532 PRO* 4.5 9.6 - - - -
992 HIS* 3.4 5.5 - - - +
1002 PHE 3.4 1.9 + - - -
1012 LEU* 3.0 39.1 + - - +
2102 MET* 4.1 20.6 - - - -
2512 PHE* 1.3 77.9 - - - +
2532 GLY* 1.3 63.8 + - - +
2542 ALA 3.7 0.9 - - - -
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Residues in contact with GLY 253 (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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512 ASP* 2.9 20.1 + - - -
992 HIS* 3.4 1.3 - - - -
1002 PHE* 3.0 32.5 + - - +
1012 LEU* 5.7 1.3 - - - -
2522 SER* 1.3 74.6 + - - +
2542 ALA* 1.3 65.5 + - - +
2552 ARG* 3.6 6.8 - - - +
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Residues in contact with ALA 254 (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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512 ASP* 4.6 1.6 + - - -
982 TYR* 3.6 2.7 - - + +
992 HIS* 3.5 28.4 - - + +
2532 GLY* 1.3 74.6 - - - +
2552 ARG* 1.3 66.4 + - - +
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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
------------------------------------------------------------
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