Contacts of the helix formed by residues 127 - 141 (chain 4) in PDB entry 5KZ5
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 ALA 127 (chain 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264 GLY* 1.4 70.2 - - - -
1284 THR* 1.4 64.0 + - - +
1294 GLU* 4.0 0.2 + - - -
1304 SER* 3.8 1.7 - - - -
1314 ASN* 3.0 33.9 + - - +
1564 HIS* 3.7 17.0 - - + +
2354 GLN* 3.9 3.8 - - - +
2554 SER* 3.6 27.7 + - - +
2574 HIS* 3.6 34.3 + - + +
2644 GLY* 4.8 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971 TRP* 5.0 5.8 - - + +
1001 GLU* 3.3 23.8 + - - +
1274 ALA* 1.4 78.4 + - + +
1294 GLU* 1.4 75.1 + - - +
1314 ASN* 3.5 4.9 + - - +
1324 ASN* 3.3 16.6 + - - +
1564 HIS* 3.7 31.2 - - + +
1574 LYS* 5.3 1.8 - - + +
1584 CYS* 3.6 28.2 - - - +
1594 VAL* 3.7 9.7 - - - +
2574 HIS* 6.0 3.1 - - + -
118D TYR* 5.1 0.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001 GLU* 3.6 30.5 - - - +
1041 GLU* 3.3 31.8 - - + +
1244 THR* 5.7 0.7 - - - -
1254 SER 3.3 22.9 - - - +
1264 GLY* 3.2 20.2 - - - +
1274 ALA 4.0 0.2 + - - -
1284 THR* 1.4 94.3 + - - +
1304 SER* 1.4 63.1 + - - +
1324 ASN* 3.5 3.0 - - - +
1334 ILE* 3.2 32.1 + - + +
1584 CYS* 5.7 1.1 - - - -
2794 GLU* 5.6 0.4 - - - +
117D PRO* 4.4 12.9 - - + +
118D TYR* 3.8 21.5 + - - -
456P GLN* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1244 THR* 3.1 32.9 + - - -
1254 SER 4.4 0.5 + - - -
1264 GLY 2.9 22.9 + - - -
1274 ALA* 3.8 8.2 - - - -
1284 THR 3.4 0.4 - - - -
1294 GLU* 1.4 76.8 - - - +
1314 ASN* 1.4 61.3 + - - +
1334 ILE* 3.7 0.9 + - - +
1344 ALA* 3.3 18.9 + - - +
2534 SER* 3.4 18.4 + - - -
2544 ILE 4.8 4.0 - - - -
2554 SER* 4.4 7.2 + - - -
2664 GLY* 4.6 2.9 - - - -
2674 ALA 4.5 7.9 - - - -
2684 ILE* 3.8 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 131 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274 ALA* 3.0 23.6 + - - +
1284 THR 3.7 5.2 - - - +
1304 SER* 1.4 77.5 - - - +
1324 ASN* 1.4 65.2 + - - +
1344 ALA* 3.3 2.3 + - - +
1354 ILE* 3.2 32.6 + - + +
1564 HIS* 3.4 22.1 + - + +
1594 VAL* 4.2 8.3 - - + -
2034 MET* 3.7 8.7 - - + +
2304 HIS* 3.3 18.2 - - - -
2324 ASP* 3.0 42.2 + - - +
2344 ALA* 4.5 5.1 - - - +
2534 SER* 3.6 8.4 + - - -
2554 SER* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041 GLU* 3.2 28.0 + - - +
1284 THR 3.3 11.7 + - - +
1294 GLU* 3.5 9.2 - - - +
1314 ASN* 1.4 77.9 - - - +
1334 ILE* 1.3 61.0 + - - +
1354 ILE* 3.4 0.7 + - - +
1364 LYS* 3.2 36.0 + - - +
1594 VAL* 3.7 22.2 - - + +
1624 SER* 4.8 0.3 - - - -
456P GLN* 3.2 35.3 - - - +
457P HIS* 3.2 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041 GLU* 3.4 18.4 - - - +
1081 GLN* 5.6 2.0 - - - +
1181 PRO* 5.4 4.1 - - + +
1244 THR* 3.7 13.9 - - + -
1294 GLU* 3.2 20.5 + - + +
1304 SER 4.0 3.4 - - - +
1324 ASN* 1.3 77.6 - - - +
1344 ALA* 1.4 57.6 + - - +
1364 LYS* 3.9 4.6 - - - +
1374 GLY* 3.0 26.3 + - - -
2684 ILE* 3.9 13.2 - - + +
2784 VAL* 3.5 37.8 - - + +
2794 GLU* 3.3 42.2 - - + +
457P HIS* 5.1 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1304 SER 3.3 12.8 + - - +
1314 ASN 3.6 7.2 - - - +
1324 ASN 3.3 0.2 - - - -
1334 ILE* 1.4 74.7 - - - +
1354 ILE* 1.4 57.7 - - - +
1374 GLY* 3.3 2.3 + - - -
1384 VAL* 3.2 33.2 + - - +
2304 HIS* 3.5 31.6 - - + +
2514 LEU* 4.4 4.3 - - + +
2524 MET 4.8 1.8 - - - +
2534 SER* 3.8 8.3 - - - +
2684 ILE* 3.6 22.3 - - + +
2694 TYR 5.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1314 ASN* 3.2 25.9 + - + +
1324 ASN 3.8 3.4 - - - +
1344 ALA* 1.4 71.3 - - - +
1364 LYS* 1.3 87.7 + - + +
1384 VAL* 3.4 2.6 + - - -
1394 ALA* 3.4 17.8 + - - +
1514 THR* 5.1 1.1 - - + -
1554 GLU* 3.8 25.4 - - + +
1594 VAL* 3.9 11.2 - - + -
1994 LEU* 3.4 35.7 - - + +
2014 SER* 3.3 28.5 - - - +
2034 MET* 5.2 0.9 - - - -
2304 HIS* 3.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 ASP* 3.3 28.4 - - + +
1181 PRO* 5.1 2.5 - - + -
1324 ASN* 3.2 31.7 + - - +
1334 ILE* 4.0 3.8 - - - +
1354 ILE* 1.3 99.1 - - + +
1374 GLY* 1.4 59.9 + - - +
1394 ALA* 3.2 18.3 + - - +
1404 ARG 3.3 4.9 + - - -
1494 LEU* 5.7 7.5 - - - +
1514 THR* 5.1 1.0 - - - +
1594 VAL* 4.4 2.2 - - - +
1624 SER* 6.3 0.2 - - - -
1634 CYS* 3.4 30.3 - - - -
1664 LEU* 6.2 4.4 - - - +
1994 LEU* 4.9 6.1 - - - +
456P GLN 4.5 4.2 + - - +
457P HIS* 3.4 50.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181 PRO* 5.4 2.7 - - - +
1334 ILE 3.0 19.2 + - - -
1344 ALA 3.7 2.2 - - - -
1354 ILE 3.3 0.4 - - - -
1364 LYS* 1.4 72.7 - - - +
1384 VAL* 1.4 62.2 + - - +
1404 ARG* 3.6 4.8 + - - +
1414 PHE* 3.2 23.7 + - - +
2514 LEU* 4.3 7.0 - - - +
2704 ILE* 4.6 7.2 - - - +
2764 VAL* 5.4 2.4 - - - +
2784 VAL* 4.3 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1344 ALA 3.2 16.2 + - - +
1354 ILE 3.5 8.7 - - - +
1374 GLY* 1.4 72.2 - - - +
1394 ALA* 1.4 65.1 + - - +
1414 PHE* 3.4 11.9 + - - +
1424 TYR* 3.5 7.8 + - - +
1984 SER 3.3 18.4 - - - +
1994 LEU* 3.5 12.6 - - + -
2284 TYR* 3.2 36.5 - - + +
2304 HIS* 4.4 16.2 - - + +
2514 LEU* 3.6 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 ASP* 3.9 11.9 - - - +
1354 ILE 3.4 9.0 + - - +
1364 LYS* 3.2 16.3 + - - +
1384 VAL* 1.4 78.3 - - - +
1404 ARG* 1.3 61.2 + - - +
1434 ARG* 3.4 18.7 + - - +
1494 LEU* 3.5 30.6 - - + +
1984 SER* 3.3 21.3 + - - -
1994 LEU* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151 GLY 2.4 29.7 + - - -
1161 ALA* 2.8 29.2 + - - +
1171 ASP* 3.5 21.3 + - + +
1181 PRO 5.2 0.4 - - - +
1191 ARG* 4.1 21.8 - - + -
1201 GLU* 3.3 31.1 + - + -
2441 VAL* 4.3 3.0 - - - +
2451 ASN* 3.4 13.9 - - - +
2721 ARG* 3.4 16.9 - - - +
2731 ARG* 3.4 12.0 + - - +
1364 LYS 3.3 4.6 + - - +
1374 GLY* 3.6 4.7 + - - +
1384 VAL 3.3 0.2 - - - -
1394 ALA* 1.3 79.2 - - - +
1414 PHE* 1.3 65.0 + - - +
1424 TYR 3.5 0.2 - - - -
1434 ARG* 3.1 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191 ARG* 6.3 0.2 - - - -
2721 ARG* 3.3 51.0 + - - +
2731 ARG* 2.8 21.7 + - - -
1374 GLY 3.2 17.4 + - - +
1384 VAL* 3.7 8.5 - - - +
1394 ALA 3.4 0.4 - - - -
1404 ARG* 1.3 77.1 - - - +
1424 TYR* 1.3 61.3 + + - +
2284 TYR* 3.8 39.9 - + + -
2514 LEU* 5.1 7.9 - - + -
2714 ARG* 3.2 33.9 - - + -
2724 ARG 4.7 0.4 - - - -
2734 ARG 3.9 20.4 - - - -
2744 PRO* 3.8 9.9 - - + -
2764 VAL* 4.1 15.7 - - + -
----------------------------------------------------------
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