Contacts of the helix formed by residues 127 - 141 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261 GLY* 1.4 69.3 - - - -
1281 THR* 1.4 60.8 + - - +
1291 GLU 3.4 0.2 - - - -
1301 SER* 3.3 5.0 + - - -
1311 ASN* 2.9 36.2 + - - +
2321 ASP* 4.8 0.2 - - - +
2341 ALA* 4.2 3.4 - - + -
2531 SER* 3.1 18.9 + - - +
2541 ILE 4.3 1.1 - - - -
2551 SER* 3.3 26.6 - - - +
2571 HIS* 5.2 3.6 - - + +
2581 LYS* 3.8 31.4 - - + +
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Residues in contact with THR 128 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261 GLY* 4.5 0.9 - - - -
1271 ALA* 1.4 77.5 + - - +
1291 GLU* 1.4 59.9 + - - +
1311 ASN* 3.4 5.9 + - - +
1321 ASN* 3.0 27.7 + - - -
1561 HIS* 3.5 35.8 + - + +
2571 HIS* 5.2 10.1 - - + +
2581 LYS* 3.8 24.7 - - - +
972 TRP* 5.4 9.6 - - + -
1042 GLU* 3.3 11.0 + - - -
118G TYR* 3.2 19.9 + - - -
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Residues in contact with GLU 129 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 THR* 3.6 15.7 - - + +
1251 SER 3.4 23.9 + - - -
1261 GLY 3.3 11.0 - - - +
1281 THR* 1.4 78.3 + - - +
1301 SER* 1.4 62.5 + - - +
1321 ASN* 3.5 5.5 - - - +
1331 ILE* 3.2 27.1 + - - +
2811 LEU* 3.8 20.0 - - + +
1002 GLU* 4.7 0.2 - - - +
1042 GLU* 3.4 21.5 + - + +
1072 ARG* 3.4 20.9 + - - +
117G PRO* 4.0 14.0 - - - +
118G TYR* 3.3 29.4 + - - +
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Residues in contact with SER 130 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 THR* 3.3 13.3 + - - -
1261 GLY 3.1 14.6 + - - -
1271 ALA* 3.3 11.7 + - - -
1291 GLU* 1.4 77.5 - - - +
1311 ASN* 1.4 62.2 + - - +
1331 ILE* 4.0 6.5 - - - -
1341 ALA* 3.3 24.4 + - - +
2301 HIS* 4.2 1.0 + - - -
2531 SER* 3.5 16.4 - - - -
2541 ILE 4.3 1.2 + - - -
2671 ALA 3.1 24.3 + - - -
2681 ILE* 3.4 13.5 - - - +
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Residues in contact with ASN 131 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271 ALA* 2.9 26.0 + - - +
1281 THR* 3.7 8.8 - - - +
1301 SER* 1.4 72.2 - - - +
1321 ASN* 1.4 65.6 + - - +
1351 ILE* 3.2 36.2 + - + +
1561 HIS* 4.4 14.0 - - + +
1591 VAL* 3.8 16.7 - - + +
2071 ASN* 4.6 4.4 - - - +
2301 HIS* 3.2 18.2 - - - -
2321 ASP* 3.4 24.8 + - - +
2531 SER* 3.0 21.2 + - - -
2581 LYS* 5.0 1.4 - - - +
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Residues in contact with ASN 132 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281 THR 3.0 15.9 + - - +
1291 GLU* 3.5 11.9 - - - +
1311 ASN* 1.4 79.6 - - - +
1331 ILE* 1.3 62.8 + - + +
1361 LYS* 3.4 16.3 + - - +
1561 HIS* 3.7 2.0 + - - -
1581 CYS* 3.4 23.5 - - - +
1591 VAL* 3.4 13.8 - - - +
1042 GLU* 3.2 37.3 + - + +
1082 GLN* 3.1 49.7 + - + +
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Residues in contact with ILE 133 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 THR* 6.0 0.7 - - + -
1291 GLU 3.3 16.4 - - - +
1301 SER* 3.5 10.3 - - - +
1321 ASN* 1.3 79.1 - - + +
1341 ALA* 1.4 64.5 + - - +
1371 GLY 3.5 5.7 + - - -
2681 ILE* 3.8 22.4 - - + -
2781 VAL* 3.3 26.5 - - + +
2791 GLU* 2.9 53.0 - - + +
2801 ALA 3.2 26.9 - - - +
2811 LEU* 4.5 16.8 - - + -
1082 GLN* 5.3 2.7 - - - -
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Residues in contact with ALA 134 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1301 SER 3.3 14.1 + - - +
1311 ASN 4.1 0.4 - - - +
1321 ASN 3.4 0.6 - - - -
1331 ILE* 1.4 85.5 - - - +
1351 ILE* 1.3 64.0 + - - +
1381 VAL* 3.1 27.9 + - - +
1991 LEU* 5.4 0.2 - - - +
2301 HIS* 3.2 33.8 - - + +
2511 LEU* 3.7 20.1 - - + +
2681 ILE* 3.9 9.9 - - + -
2791 GLU* 5.0 0.9 - - - -
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Residues in contact with ILE 135 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311 ASN* 3.2 24.2 + - + +
1321 ASN 4.6 0.2 - - - +
1341 ALA* 1.3 76.6 - - - +
1361 LYS* 1.3 61.0 + - - +
1391 ALA* 3.2 25.8 + - - +
1551 GLU* 3.6 30.1 - - + +
1591 VAL* 3.7 23.8 - - + -
1631 CYS* 4.7 6.3 - - - -
1991 LEU* 3.7 34.2 - - + +
2011 SER* 3.9 7.6 - - - +
2301 HIS* 3.5 39.9 - - + +
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Residues in contact with LYS 136 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1321 ASN 3.4 15.5 + - - +
1351 ILE* 1.3 77.7 + - + +
1371 GLY* 1.3 66.0 + - - +
1391 ALA* 3.2 20.4 + - + +
1401 ARG* 3.5 7.4 + - - +
1491 LEU* 4.8 2.8 - - - +
1591 VAL* 6.1 0.2 - - + -
1621 SER* 3.4 37.2 - - - +
1631 CYS* 3.6 28.4 - - - +
1661 LEU* 3.3 31.4 - - + +
1991 LEU* 5.3 2.0 - - - +
1082 GLN* 3.7 22.4 - - + +
1122 SER* 3.5 31.2 + - - +
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Residues in contact with GLY 137 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331 ILE* 3.5 8.3 + - - +
1351 ILE 3.5 0.4 - - - -
1361 LYS* 1.3 78.1 - - - +
1381 VAL* 1.4 60.9 + - - +
1401 ARG* 4.0 0.3 + - - +
1411 PHE* 3.4 24.9 + - - +
2791 GLU* 3.3 30.2 + - - -
1112 ALA* 5.6 0.2 - - - -
1122 SER* 5.3 8.9 - - - -
1162 ALA 3.6 7.3 + - - +
1172 ASP* 3.6 7.4 - - - -
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Residues in contact with VAL 138 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341 ALA 3.1 21.8 + - - +
1351 ILE 3.9 2.7 - - - +
1371 GLY* 1.4 75.4 - - - +
1391 ALA* 1.3 63.3 + - - +
1421 TYR* 3.3 27.4 + - + +
1981 SER* 3.1 28.6 + - - +
1991 LEU* 4.3 11.2 - - + -
2281 TYR* 3.9 20.2 - - + -
2511 LEU* 4.0 26.5 - - + -
2791 GLU* 5.6 0.4 - - - +
1172 ASP* 3.6 27.0 - - + +
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Residues in contact with ALA 139 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351 ILE 3.2 15.5 + - - +
1361 LYS* 3.2 28.6 + - + +
1381 VAL* 1.3 79.6 - - - +
1401 ARG* 1.4 63.7 + - - +
1431 ARG* 4.0 5.0 - - - +
1491 LEU* 3.2 28.0 - - + +
1661 LEU* 4.6 0.2 - - + -
1981 SER* 3.1 22.9 + - - -
1991 LEU* 3.9 14.1 - - + -
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Residues in contact with ARG 140 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361 LYS 3.5 5.6 + - - +
1371 GLY 5.1 0.2 - - - +
1391 ALA* 1.4 77.9 - - - +
1411 PHE* 1.4 66.1 + - - +
1431 ARG* 3.2 26.1 - - - +
1661 LEU* 3.3 28.0 - - + +
1691 GLU* 3.4 24.3 + - - -
1711 PHE* 4.0 18.2 - - + -
1092 GLN* 5.0 4.9 + - - +
1122 SER* 3.3 47.2 + - - +
1132 LEU* 3.5 25.7 - - - +
2412 PRO* 3.4 26.1 - - - +
2422 LEU 3.8 6.5 - - - +
2432 ASP* 3.1 30.2 - - - +
447M ILE* 6.3 1.2 - - - +
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Residues in contact with PHE 141 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 GLY 3.4 19.8 + - - +
1401 ARG* 1.4 77.5 - - - +
1421 TYR* 1.3 59.8 + - + +
1431 ARG 3.5 1.0 + - - -
1441 SER 4.5 0.2 + - - -
1152 GLY* 3.7 6.2 - - - -
1162 ALA* 3.1 28.2 - - - +
1172 ASP* 3.5 25.1 - - - +
1182 PRO* 4.0 16.8 - - + -
1202 GLU* 4.0 15.7 - - - -
2432 ASP* 3.5 6.5 + - + -
2442 VAL* 3.9 26.0 - - + -
2452 ASN* 3.5 44.5 + - + +
2462 ASP 4.1 1.6 + - - -
2712 ARG* 4.0 16.2 - - + -
2732 ARG* 3.7 22.9 - - - -
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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
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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