Contacts of the strand formed by residues 125 - 142 (chain 1) 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 PHE 125 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 ILE* 3.9 19.1 - - + -
801 PHE* 5.1 5.4 - + - -
811 PHE* 4.1 21.1 - + - -
1211 LYS 4.2 2.2 - - - -
1221 LEU 3.1 12.4 + - - +
1231 GLU 3.0 0.6 - - - -
1241 PHE* 1.4 105.0 - + + +
1261 THR* 1.3 59.8 + - - +
1271 TYR 4.0 4.9 - - - +
2071 HIS* 2.8 26.6 + + - +
2081 PHE* 3.9 6.2 - - - -
2691 VAL* 3.6 41.7 - - + -
2701 TRP 3.7 10.8 - - - +
2711 CYS 3.6 3.4 - - - -
2721 PRO* 4.1 23.3 - - + -
2731 ARG* 4.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251 PHE* 1.3 72.4 - - - +
1271 TYR* 1.3 75.9 + - + +
2061 SER* 3.9 0.2 - - - -
2071 HIS* 2.8 28.8 + - - +
2081 PHE* 4.2 6.3 - - + -
2701 TRP 3.1 0.8 + - - -
2711 CYS* 2.9 34.2 + - + +
2731 ARG* 3.0 31.1 + - - +
1282 PRO* 4.2 5.6 - - + +
1292 GLU* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251 PHE* 4.0 2.8 - - - +
1261 THR* 1.3 101.9 - - + +
1281 SER* 1.3 62.0 + - - +
2041 ALA* 3.9 11.9 - - + -
2051 TYR 3.2 11.4 - - - +
2061 SER* 3.9 12.6 - - - -
2071 HIS* 4.4 2.2 - - - +
2691 VAL* 3.5 4.9 - - - +
2701 TRP* 3.0 49.9 + + + +
2711 CYS* 4.2 4.3 - - - -
1282 PRO* 4.8 1.0 - - - +
1292 GLU* 2.7 34.3 + - + +
2122 VAL* 3.7 27.9 + - + +
2132 ASN* 3.4 24.3 + - - -
2142 ALA* 3.8 27.1 - - + -
2252 ASN 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221 LEU* 5.2 0.7 - - - -
1271 TYR* 1.3 75.8 - - - +
1291 ARG* 1.3 63.4 + - - +
1301 PHE* 3.2 26.0 - - - -
2041 ALA* 3.5 1.4 - - - -
2051 TYR* 2.8 36.5 + - - +
2071 HIS* 2.7 33.2 + - - -
2681 ARG 3.3 11.7 - - - -
2691 VAL* 4.0 8.7 - - - -
2701 TRP* 4.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281 SER* 1.3 75.3 - - - +
1301 PHE* 1.3 62.8 + - - +
1981 TYR* 3.4 47.6 - - + +
2031 ASN* 3.1 32.3 + - - +
2051 TYR* 4.6 0.4 - - - -
2661 HIS 3.6 3.0 - - - +
2671 VAL* 3.6 0.9 - - - -
2681 ARG* 2.9 46.4 + - + +
2701 TRP* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221 LEU* 3.9 25.1 - - + -
1281 SER* 3.2 30.5 - - - -
1291 ARG* 1.3 78.7 - - - +
1311 ASP* 1.3 76.0 + - - +
1321 MET* 3.6 28.7 - - + +
1971 PRO 4.3 0.5 - - - +
1981 TYR* 3.5 27.8 - - - +
2051 TYR* 3.7 24.9 + + - -
2071 HIS* 4.7 1.3 - - - -
2641 PRO* 3.8 15.0 - - + -
2651 LYS 3.7 9.0 - - - +
2661 HIS 3.6 9.4 - - - -
2671 VAL* 4.1 20.6 - - + -
10001 SPH 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1301 PHE* 1.3 81.1 - - - +
1321 MET* 1.3 61.4 + - - +
1961 VAL 3.4 9.2 - - - +
1971 PRO* 3.3 21.6 - - - +
1981 TYR* 3.3 8.1 + - - +
2641 PRO* 3.6 0.2 - - - +
2651 LYS* 2.9 39.4 + - + +
2661 HIS* 2.7 32.3 + - - +
364 SER* 4.2 3.6 + - - +
374 ALA* 3.6 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 132 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121 TYR* 6.0 0.4 - - + -
1181 LEU* 5.3 3.1 - - + -
1221 LEU* 5.9 2.9 - - + -
1301 PHE* 3.6 30.7 - - + -
1311 ASP* 1.3 73.4 - - - +
1331 GLU* 1.3 59.5 + - - +
1341 PHE* 3.5 32.5 + - + -
1941 ILE 4.0 0.3 - - - +
1951 SER* 3.3 3.6 - - - -
1961 VAL* 2.9 42.2 + - + +
1971 PRO 4.8 0.9 + - - +
2051 TYR* 6.1 0.2 - - - +
2621 MET* 3.5 43.3 - - + -
2631 LYS 3.7 19.5 - - - +
2641 PRO* 3.9 9.2 - - + -
2651 LYS* 4.9 2.2 - - - -
10001 SPH 4.2 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841 GLY* 5.8 0.9 - - - -
1321 MET* 1.3 74.0 - - - +
1341 PHE* 1.3 60.3 + - - +
1351 THR* 3.7 5.7 + - - +
1931 ARG* 3.3 50.6 + - + -
1941 ILE 3.4 10.5 - - - +
1951 SER* 4.3 7.2 - - - +
2611 TYR 3.6 1.0 - - - +
2621 MET* 3.5 5.4 - - - -
2631 LYS* 3.0 70.6 + - + +
2651 LYS* 4.2 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081 TRP* 4.7 4.9 - + - -
1101 ILE* 4.4 7.9 - - + -
1321 MET* 3.5 26.2 - - + -
1331 GLU* 1.3 76.5 - - - +
1351 THR* 1.3 61.6 + - - +
1361 PHE* 3.8 26.1 - + + -
1931 ARG* 3.2 5.1 - - - +
1941 ILE* 2.9 50.0 + - + -
1961 VAL* 4.6 3.4 - - + -
2411 LEU* 5.1 3.8 - - + -
2601 ILE* 3.6 25.4 - - + -
2611 TYR 3.4 4.3 - - - -
2621 MET* 3.8 35.4 - - + -
10001 SPH 4.0 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331 GLU* 3.7 6.6 + - - -
1341 PHE* 1.3 73.0 - - - +
1361 PHE* 1.3 63.2 + - - +
1371 VAL* 5.2 4.0 - - + -
1911 PRO* 3.8 21.1 - - + -
1921 ALA 3.2 11.4 - - - +
1931 ARG* 3.0 37.9 + - - +
2601 ILE* 3.7 2.3 - - - +
2611 TYR* 2.9 47.4 + - + +
83 PRO* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341 PHE* 3.8 34.3 - + + -
1351 THR* 1.3 73.9 - - - +
1371 VAL* 1.3 61.4 + - - +
1381 VAL* 4.0 8.2 + - + +
1571 ILE* 3.9 27.6 - - + -
1831 ILE* 3.5 32.1 - - + -
1851 TYR* 5.0 1.7 - - + -
1911 PRO* 3.3 8.3 - - - +
1921 ALA* 2.9 46.9 + - + +
1941 ILE* 4.2 3.4 - - + -
2411 LEU* 4.1 12.8 - - + -
2581 VAL* 4.1 11.7 - - + -
2591 ARG 3.5 3.6 - - - +
2601 ILE* 3.8 37.5 - - + -
10001 SPH 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1351 THR* 5.2 3.1 - - + -
1361 PHE* 1.3 74.0 - - - +
1381 VAL* 1.3 62.4 + - - +
1391 THR* 4.7 14.9 + - + -
1911 PRO* 4.1 25.6 - - + -
2571 LYS 3.7 1.6 - - - +
2581 VAL* 3.6 1.2 - - - -
2591 ARG* 2.9 42.4 + - + +
2611 TYR* 3.6 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361 PHE* 4.0 10.0 + - + +
1371 VAL* 1.3 79.3 - - - +
1391 THR* 1.3 68.0 + - - +
1551 TYR* 3.7 44.2 - - + +
1571 ILE* 5.4 2.9 - - + -
1851 TYR* 3.5 41.0 + - + -
1871 TYR* 3.6 14.7 - - + -
1881 GLY 5.7 0.2 + - - -
1911 PRO* 6.0 0.2 - - - +
2561 SER* 4.8 0.2 - - - -
2571 LYS 3.4 8.3 - - - +
2581 VAL* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1371 VAL* 4.7 14.4 + - + -
1381 VAL* 1.3 77.4 - - - +
1401 ALA* 1.3 60.9 + - - +
1871 TYR* 3.6 9.0 - - - +
2561 SER* 3.2 5.2 - - - -
2571 LYS* 3.0 37.7 + - - +
2591 ARG* 3.8 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391 THR* 1.3 75.4 - - - +
1411 ASN* 1.3 66.3 + - - +
1531 GLN* 5.1 0.2 - - - +
1551 TYR* 3.9 3.4 - - - +
1871 TYR* 2.9 33.7 + - + +
2541 VAL* 4.1 12.8 - - + -
2551 THR 3.2 7.4 - - - +
2561 SER* 3.6 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1401 ALA* 1.3 78.6 - - - +
1421 PHE* 1.3 83.7 + - - +
1431 THR* 4.2 10.5 - - - +
2541 VAL* 3.7 7.6 - - - +
2551 THR* 3.0 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1411 ASN* 1.3 90.1 + - - +
1431 THR* 1.3 61.2 + - - +
1441 ASN 4.2 13.0 - - - +
1481 GLY 5.2 0.4 - - - -
1491 HIS* 3.8 25.1 - + + -
1501 ALA* 4.1 25.4 - - + -
2521 THR* 3.7 34.5 - - + -
2531 LYS 4.1 8.7 - - - -
2541 VAL* 4.2 7.0 - - + -
----------------------------------------------------------
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