Contacts of the strand formed by residues 245 - 262 (chain 2) in PDB entry 3EPD
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 GLU 245 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702 MET* 4.0 33.8 - - + +
712 TRP 3.1 11.7 - - - +
722 GLY* 4.1 10.0 + - - -
2362 LEU* 4.1 0.9 - - - -
2432 SER 3.5 7.9 + - - +
2442 VAL* 1.3 80.0 - - - +
2462 ILE* 1.3 68.3 + - - +
2472 PRO* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702 MET* 4.2 4.3 - - - -
712 TRP* 2.8 43.6 + - + +
1122 CYS* 3.6 25.1 - - - -
1132 ASN 3.8 17.5 - - - +
1142 ALA* 3.8 17.3 - - + -
1182 HIS* 4.2 23.3 - - + +
1992 LEU* 4.0 3.4 - - + -
2362 LEU* 3.9 23.6 - - + -
2442 VAL* 4.8 1.1 - - + -
2452 GLU* 1.3 78.5 - - - +
2472 PRO* 1.3 70.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 247 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682 THR* 3.4 21.5 - - + -
692 VAL 3.5 6.7 - - - +
702 MET* 3.9 18.8 - - + -
1112 GLN 4.0 0.6 - - - +
1122 CYS* 3.5 24.3 - - - -
1132 ASN* 4.9 6.7 + - - +
2452 GLU 4.8 0.4 - - - +
2462 ILE* 1.3 93.2 - - + +
2482 ILE* 1.3 58.9 + - - +
2492 THR* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672 ASP 4.9 0.2 - - - +
682 THR* 3.6 0.9 - - - -
692 VAL* 2.9 42.1 + - + +
712 TRP* 3.8 18.2 - - + -
782 TRP* 3.5 42.4 - - + -
1102 VAL* 4.0 25.8 - - + -
1112 GLN 3.4 6.7 - - - +
1122 CYS* 4.1 11.7 - - - -
1222 LEU* 3.8 19.3 - - + -
2302 ILE* 4.4 12.3 - - + -
2472 PRO* 1.3 77.7 - - - +
2492 THR* 1.3 64.4 + - - +
2502 VAL* 4.4 5.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 THR* 3.5 31.0 - - + -
662 LEU 4.4 2.0 - - - +
682 THR* 2.9 31.8 + - - +
1102 VAL* 3.6 1.6 - - - +
1112 GLN* 2.8 58.9 + - - +
2472 PRO* 4.2 3.5 - - - +
2482 ILE* 1.3 73.4 + - - +
2502 VAL* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 THR* 3.7 1.0 - - - +
662 LEU* 3.1 45.4 + - + +
672 ASP 5.4 1.8 + - - +
692 VAL* 6.1 0.2 - - + -
802 TRP* 4.0 31.6 - - + -
1082 VAL* 4.7 11.7 - - + -
1092 HIS 3.7 3.4 - - - +
1102 VAL* 4.4 9.0 - - + -
2282 ILE* 5.6 4.3 - - + -
2302 ILE* 4.1 18.4 - - + -
2482 ILE* 4.4 5.4 + - + +
2492 THR* 1.3 77.3 - - - +
2512 THR* 1.3 63.6 + - - +
2522 ILE* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 ILE* 3.8 14.6 - - + -
632 PHE* 3.6 36.6 - - + -
642 TYR 3.4 5.8 - - - +
652 THR* 2.9 30.5 + - - +
1072 THR 4.0 0.5 - - - +
1082 VAL 3.7 0.2 - - - -
1092 HIS* 2.8 36.7 + - - +
1112 GLN* 2.9 26.0 + - - -
2502 VAL* 1.3 72.3 + - - +
2522 ILE* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 ARG 3.8 0.5 - - - +
632 PHE* 4.1 2.2 - - - -
642 TYR* 2.9 35.9 + - - +
662 LEU* 4.4 15.3 - - + -
802 TRP* 5.8 2.2 - - + -
822 LEU* 3.8 25.6 - - + -
852 ALA* 4.9 2.2 - - + -
862 LEU* 4.0 19.4 - - + +
1062 TYR* 3.9 31.4 - - + -
1072 THR 3.3 9.9 - - - +
1082 VAL* 4.3 15.0 - - + -
2282 ILE* 5.1 5.6 - - + -
2502 VAL* 3.8 24.9 - - + +
2512 THR* 1.3 79.3 - - - +
2532 ALA* 1.3 61.9 + - - +
2542 PRO* 4.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LEU* 3.5 28.0 - - + -
622 ARG 3.2 23.6 - - - +
632 PHE* 3.6 13.2 - - + -
1062 TYR* 3.1 6.7 - - - -
1072 THR 2.9 30.9 + - - +
2522 ILE* 1.3 73.5 - - - +
2542 PRO* 1.3 67.2 - - - +
2552 MET* 4.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 254 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LEU* 4.7 0.2 - - - +
602 THR 3.3 26.0 - - - +
612 CYS* 3.2 23.1 - - - +
622 ARG 3.5 7.0 - - - +
642 TYR* 3.8 12.1 - - + -
862 LEU* 3.7 20.0 - - + -
922 PHE* 3.5 24.9 - - + -
1042 SER* 3.5 14.4 - - - +
1052 GLY 3.5 7.4 - - - +
1062 TYR* 3.9 4.9 - - + -
2532 ALA* 1.3 88.4 - - - +
2552 MET* 1.3 62.5 + - - +
2572 SER* 3.6 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 255 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LEU* 4.2 26.7 - - + -
382 TRP* 3.9 36.6 - - + +
392 PRO* 3.8 23.3 - - + -
612 CYS* 4.0 4.7 - - - -
1042 SER* 3.5 1.1 + - - -
1052 GLY* 2.8 35.4 + - - +
1062 TYR 3.9 3.4 - - - +
1072 THR* 3.2 33.2 - - - +
2082 VAL* 4.4 3.1 - - - -
2532 ALA 4.0 5.4 - - - +
2542 PRO* 1.3 79.2 - - - +
2562 CYS* 1.3 70.8 + - - +
2572 SER 3.3 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 256 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382 TRP* 6.1 0.9 - - - -
392 PRO* 3.9 27.8 - - + -
402 GLU* 4.0 29.7 - - - +
412 PHE* 3.7 36.2 - - + -
612 CYS* 4.0 6.2 - - - -
1032 ARG* 3.8 9.9 - - - +
1042 SER* 4.3 2.3 - - - -
1052 GLY 4.8 0.6 + - - +
2552 MET* 1.3 76.9 - - - +
2572 SER* 1.3 63.6 + - - +
2582 GLU* 3.5 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 257 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412 PHE* 3.6 9.1 - - - -
552 GLU* 3.7 15.8 - - - +
562 PRO* 3.9 2.2 - - - +
572 ASP 5.2 1.0 + - - -
602 THR* 4.0 8.5 + - - -
612 CYS* 3.4 24.2 - - - -
922 PHE* 4.2 1.9 - - - -
1032 ARG 3.3 8.3 - - - -
1042 SER* 3.0 19.6 + - - -
2542 PRO* 3.6 8.3 - - - +
2562 CYS* 1.3 74.3 - - - +
2582 GLU* 1.3 60.5 + - - +
2592 PHE* 3.8 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412 PHE* 3.2 19.7 - - + +
422 ILE* 3.0 54.2 + - + +
532 PRO* 3.9 22.1 - - + +
542 THR 3.3 11.7 - - - +
552 GLU* 4.0 13.3 - - + +
1022 GLY* 3.5 1.7 - - - -
1032 ARG* 2.9 47.4 + - + +
2172 ILE* 4.0 5.6 - - + +
2562 CYS 3.5 0.8 + - - +
2572 SER* 1.3 75.5 - - - +
2592 PHE* 1.3 64.2 + - - +
2602 ASN* 4.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 259 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522 GLN 4.8 0.2 - - - +
532 PRO* 3.2 7.8 - - - +
542 THR* 3.1 31.2 + - - +
562 PRO* 3.9 22.4 - - + -
602 THR* 5.0 2.0 - - + -
922 PHE* 4.1 19.3 - + - -
952 ASN* 3.8 33.7 - - + -
962 MET* 3.9 16.8 - - + -
992 HIS* 3.5 28.1 - - + +
1012 LEU 3.3 7.0 - - - +
1022 GLY* 3.7 15.3 - - - -
1032 ARG 5.0 1.1 - - - -
2202 MET* 4.0 21.8 - - + -
2572 SER* 3.8 29.2 - - - -
2582 GLU* 1.3 77.3 - - - +
2602 ASN* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 260 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422 ILE* 5.2 1.0 - - - +
492 PRO* 3.7 27.7 + - + +
512 ASP* 2.9 43.5 + - - +
522 GLN 5.5 0.2 - - - -
532 PRO* 3.7 19.0 - - - +
992 HIS* 3.4 7.7 - - - +
1012 LEU* 2.9 43.2 + - + +
2172 ILE* 3.3 18.4 - - - +
2582 GLU* 4.5 4.0 - - - +
2592 PHE* 1.3 78.1 + - - +
2612 GLY* 1.3 62.2 + - - +
2622 LEU 3.8 0.7 - - - -
1713 ILE* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 ASP* 2.9 19.5 + - - -
992 HIS* 3.5 1.2 - - - -
1002 TYR* 2.9 28.8 + - - +
2602 ASN* 1.3 72.9 - - - +
2622 LEU* 1.3 63.9 + - - +
2632 ARG* 3.7 5.2 + - - +
1363 PRO* 4.0 9.4 - - - +
1713 ILE* 3.6 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 ASP* 4.5 2.6 + - - -
982 TYR* 3.6 31.0 - - + +
992 HIS* 3.7 30.2 - - + +
2612 GLY* 1.3 76.0 - - - +
2632 ARG* 1.3 67.6 + - - +
1363 PRO* 3.9 5.9 - - - +
1503 LEU 4.0 11.6 - - - +
1513 GLY* 3.7 13.2 - - - -
1523 THR* 4.4 3.3 + - - -
1713 ILE* 5.6 0.2 - - - +
----------------------------------------------------------
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