Contacts of the strand formed by residues 283 - 296 (chain 3) in PDB entry 1SVA
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 PRO 283 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503 PHE* 4.9 1.1 - - + -
513 LEU 3.0 20.9 - - - +
523 ASN* 3.9 15.0 - - - +
533 PRO* 3.7 9.4 - - + -
1193 VAL* 3.5 5.6 - - - +
1203 ILE* 2.7 56.2 + - + +
2823 LEU* 1.3 97.1 - - + +
2843 ARG* 1.3 55.4 + - - +
1644 VAL* 5.2 1.3 - - + -
1884 GLN* 4.3 8.3 - - - -
1894 MET* 3.8 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503 PHE* 3.2 4.5 - - - +
513 LEU* 2.8 33.7 + - + +
1173 THR* 2.6 28.2 + - - +
1183 GLU* 3.4 9.8 - - - +
1193 VAL* 3.9 17.2 - - - +
1203 ILE* 3.2 5.4 - - - -
1503 HIS* 5.1 6.7 - - - +
1513 PHE 4.3 7.1 + - - +
1523 PHE* 3.8 20.9 - - - +
2633 ALA* 3.8 12.1 - - + -
2653 ASP* 2.5 51.6 + - - +
2823 LEU 3.9 0.2 + - - -
2833 PRO* 1.3 75.3 - - - +
2853 TYR* 1.3 61.7 + - - +
2863 PHE* 3.1 37.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 285 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483 GLU* 3.0 35.6 + - + +
493 CYS 3.8 9.0 - - - -
503 PHE* 4.3 2.0 - - + +
1163 LYS* 3.8 11.2 - - + -
1173 THR* 2.6 38.3 + - - -
1183 GLU* 2.8 17.3 + - + +
1203 ILE* 3.1 17.0 - - + +
2843 ARG* 1.3 71.8 - - - +
2863 PHE* 1.3 101.4 + - - +
2873 LYS* 3.4 19.3 - - + +
2124 PRO* 3.2 35.2 + - + -
2134 SER* 3.2 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 286 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473 VAL 3.1 3.7 - - - +
483 GLU* 3.2 3.3 - - - -
493 CYS* 2.9 52.2 + - - +
503 PHE* 4.5 1.8 - - - -
513 LEU* 4.3 10.5 - - + -
1153 VAL* 4.3 9.6 - - + -
1163 LYS 3.4 4.0 - - - +
1173 THR* 4.3 1.8 - - - -
1523 PHE* 3.7 21.1 - + + -
1543 VAL* 4.2 16.6 - - + -
2613 VAL* 3.3 33.9 - - + -
2623 SER 4.2 1.3 - - - -
2633 ALA* 3.8 12.3 - - + -
2843 ARG* 3.1 47.1 - - + -
2853 TYR* 1.3 86.7 - - - +
2873 LYS* 1.3 58.9 + - - +
2883 ILE* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463 GLU* 3.6 40.5 + - + -
473 VAL 3.2 4.5 - - - +
483 GLU* 3.9 15.2 + - + +
1143 THR* 3.4 3.2 - - + +
1153 VAL* 3.0 7.1 - - - -
1163 LYS* 2.8 62.2 + - + +
2853 TYR* 3.5 29.6 - - + +
2863 PHE* 1.3 71.0 - - - +
2883 ILE* 1.3 63.6 + - - +
2893 THR* 4.0 6.6 + - - +
2164 GLU* 3.7 23.8 + - - +
2474 GLU* 5.7 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 THR 3.4 1.6 - - - +
463 GLU* 3.3 3.0 - - - -
473 VAL* 2.8 44.3 + - + +
493 CYS* 5.0 4.3 - - - -
933 ILE* 5.1 0.4 - - + -
1123 ALA* 4.4 11.7 - - + -
1143 THR 3.3 9.9 - - - +
1153 VAL* 4.6 5.6 - - + -
1543 VAL* 4.4 17.3 - - + -
2443 LEU* 4.9 0.2 - - + -
2593 LEU* 3.8 26.2 - - + -
2613 VAL* 3.9 22.4 - - + -
2863 PHE* 4.1 16.4 - - + -
2873 LYS* 1.3 78.3 - - - +
2893 THR* 1.3 67.4 + - - +
2903 LEU* 3.7 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 289 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443 PHE* 4.2 21.8 - - + -
453 THR 3.2 9.4 - - - +
463 GLU* 4.4 17.0 + - + +
1123 ALA* 3.7 0.3 - - - -
1133 VAL* 2.9 34.3 + - + +
1143 THR* 3.0 36.1 + - - +
2873 LYS* 4.6 5.0 + - - +
2883 ILE* 1.3 76.1 - - - +
2903 LEU* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353 LEU* 6.2 1.3 - - + -
443 PHE* 3.3 8.1 - - - +
453 THR* 2.8 39.2 + - - +
473 VAL* 4.4 18.8 - - + -
953 LEU* 3.8 29.4 - - + -
1103 TRP* 4.0 17.7 - - + -
1113 GLU 3.2 6.7 - - - +
1123 ALA* 3.3 34.8 - - + +
1133 VAL* 5.0 0.9 - - - -
2543 CYS* 5.3 2.5 - - - -
2593 LEU* 4.2 18.6 - - + -
2883 ILE* 3.8 14.4 - - + +
2893 THR* 1.3 80.7 - - - +
2913 ARG* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LYS* 5.6 3.1 - - - +
433 SER 4.4 3.1 - - - +
443 PHE* 4.4 14.6 - - + +
1103 TRP* 3.5 8.0 - - - -
1113 GLU* 2.7 75.2 + - + +
1133 VAL* 3.7 23.2 - - + +
2453 LEU* 3.9 14.9 - - - +
2493 GLY 3.3 13.5 + - - -
2903 LEU* 1.3 73.9 - - - +
2923 LYS* 1.3 70.2 + - - +
2933 ARG* 3.3 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 LYS* 4.3 7.8 - - - +
182 LYS* 2.6 33.8 + - - +
383 LYS* 5.5 0.2 - - - +
393 THR* 2.7 37.0 + - - +
403 GLY 2.7 29.8 + - - +
413 VAL* 3.4 20.2 + - - +
433 SER* 3.9 13.0 + - - +
983 ILE* 3.5 37.3 - - + +
1083 LEU* 4.0 15.9 - - + -
1093 MET 3.7 4.9 - - - -
1103 TRP* 4.0 15.3 - - + -
2913 ARG* 1.3 76.5 - - - +
2933 ARG* 1.3 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LYS* 4.9 5.2 - - - +
212 VAL* 3.3 36.1 - - - +
1083 LEU* 3.2 6.0 - - - -
1093 MET* 2.7 44.2 + - - +
1113 GLU* 2.4 70.2 + - + +
2483 GLN 4.6 2.8 + - - -
2493 GLY 3.4 16.0 + - - -
2503 VAL* 3.6 17.2 - - - +
2533 LEU* 4.5 6.7 - - + -
2913 ARG* 3.3 13.1 + - + +
2923 LYS* 1.3 73.7 - - - +
2943 SER* 1.3 80.9 + - - +
2953 VAL* 3.7 7.1 + - + +
3406 LEU* 4.1 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172 PRO 4.5 0.2 - - - -
182 LYS* 2.7 46.8 + - - +
192 GLU 4.8 0.2 - - - -
202 PRO* 3.4 28.6 - - - +
212 VAL 4.7 0.2 + - - -
1063 ASN* 4.2 3.8 - - - +
1073 ILE 3.4 9.8 + - - -
1083 LEU* 3.4 13.1 - - - +
2923 LYS 4.2 0.8 + - - -
2933 ARG* 1.3 90.7 + - - +
2953 VAL* 1.3 60.1 + - - +
3406 LEU* 4.3 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202 PRO* 3.3 15.4 - - - +
1063 ASN* 3.6 3.1 - - - -
1073 ILE* 2.9 45.8 + - + +
1093 MET* 3.5 43.5 - - + -
2533 LEU* 4.0 23.3 - - + -
2933 ARG* 4.2 6.3 - - + +
2943 SER* 1.3 75.9 - - - +
2963 LYS* 1.3 62.0 + - - +
2973 ASN 4.2 1.6 - - - +
3406 LEU* 3.4 18.6 - - + +
3426 GLY* 3.6 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202 PRO* 4.8 0.9 - - - -
1053 GLY 4.1 5.2 - - - +
1063 ASN* 5.0 2.2 - - - +
2953 VAL* 1.3 74.1 - - - +
2973 ASN* 1.3 70.2 + - - +
2983 PRO* 2.7 12.8 - - - +
3386 GLU* 3.4 38.0 + - - +
3396 GLU* 3.4 46.7 + - + +
3406 LEU 3.0 14.9 + - - +
3416 PRO* 4.2 9.6 - - + +
3426 GLY 3.4 5.9 + - - -
3466 MET* 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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