Contacts of the helix formed by residues 129 - 148 (chain 7) in PDB entry 5LN3
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 SER 129 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277 SER* 5.3 1.4 - - - -
1287 TYR* 1.3 76.6 + - - +
1307 PRO* 1.3 73.8 - - - +
1317 ARG* 3.5 31.0 - - - +
1327 ALA* 3.1 10.0 + - - +
1337 ILE* 3.1 19.5 + - - +
1617 ALA* 6.3 0.4 - - - -
1627 ASP* 5.9 2.7 - - - -
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Residues in contact with PRO 130 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937 SER* 6.1 0.2 - - - +
947 THR* 3.7 22.0 - - + +
1287 TYR 4.5 1.3 - - - +
1297 SER* 1.3 88.1 - - - +
1317 ARG* 1.4 57.4 + - - +
1337 ILE* 3.2 14.7 + - + +
1347 HIS* 3.0 29.8 + - - +
1577 ILE* 5.3 2.5 - - + +
1587 GLY 6.2 0.2 - - - -
1597 GLY 5.2 0.2 - - - -
1607 TYR 3.4 31.0 - - - +
1617 ALA* 4.2 10.8 - - + +
1627 ASP* 6.0 0.4 - - - +
1667 PHE* 3.7 31.8 - - + -
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Residues in contact with ARG 131 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1297 SER* 3.5 22.6 - - - +
1307 PRO* 1.4 61.5 - - - +
1327 ALA* 1.4 62.1 + - + +
1347 HIS* 3.5 5.5 - - - +
1357 SER* 3.2 25.6 + - - -
1617 ALA* 3.8 23.8 - - - +
1627 ASP* 5.2 4.2 + - - -
1647 GLU* 4.4 22.6 + - - +
1667 PHE* 3.8 30.3 - - + -
100F ASP* 6.6 0.2 - - - -
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Residues in contact with ALA 132 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1287 TYR* 4.4 9.6 - - + -
1297 SER* 3.1 22.2 + - - +
1317 ARG* 1.4 80.6 - - + +
1337 ILE* 1.4 57.0 + - - +
1357 SER* 3.2 6.3 + - - -
1367 TRP* 2.9 30.5 + - - +
99F PHE* 3.7 38.4 - - + +
101F ARG* 5.2 5.4 - - + -
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Residues in contact with ILE 133 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907 VAL* 4.6 21.5 - - + -
917 ASN* 6.3 2.2 - - + -
947 THR* 4.8 9.0 - - + +
1127 LEU* 4.9 12.1 - - + -
1247 ASP* 5.5 7.6 - - + +
1287 TYR* 3.6 31.2 - - + +
1297 SER 3.1 17.7 + - - +
1307 PRO* 3.5 14.4 - - + +
1327 ALA* 1.4 70.4 - - - +
1347 HIS* 1.4 63.9 + - - +
1367 TRP* 3.6 8.2 - - + +
1377 LEU* 3.1 35.8 + - + +
1577 ILE* 4.0 27.4 - - + -
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Residues in contact with HIS 134 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307 PRO 3.0 16.0 + - - +
1317 ARG 3.5 7.6 - - - +
1337 ILE* 1.4 72.5 - - - +
1357 SER* 1.4 54.4 + - - +
1377 LEU* 3.2 15.3 + - - +
1387 THR* 2.8 33.3 + - - -
1577 ILE* 3.7 15.7 - - + +
1667 PHE* 4.0 22.8 - + + -
1687 GLY* 3.8 5.3 - - - -
1697 TYR 3.1 40.4 - - - -
1707 VAL* 4.3 6.4 - - + +
1767 ALA* 3.8 20.4 - - + +
1777 TYR 3.9 10.6 + - - -
1787 GLU* 4.8 2.3 - - + +
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Residues in contact with SER 135 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1317 ARG 3.2 13.4 + - - -
1327 ALA* 3.2 11.0 + - - -
1347 HIS* 1.4 77.7 - - - +
1367 TRP* 1.4 65.6 + - - +
1387 THR* 3.0 19.9 + - - -
1397 ARG* 3.1 21.5 + - - +
98F VAL 3.5 18.8 - - - -
99F PHE 4.6 0.9 + - - -
100F ASP* 3.5 18.9 + - - +
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Residues in contact with TRP 136 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087 LEU* 4.7 17.9 - - + -
1117 VAL* 4.1 17.3 - - + -
1127 LEU* 5.6 8.5 - - + -
1157 MET* 3.5 35.7 - - + +
1287 TYR* 5.7 1.3 - + + -
1327 ALA 2.9 16.5 + - - +
1337 ILE* 3.6 9.9 - - + +
1357 SER* 1.4 76.5 - - - +
1377 LEU* 1.4 79.6 + - + +
1397 ARG* 3.5 8.2 + - - +
1407 ALA* 3.4 28.2 + - + +
98F VAL* 3.9 16.5 - - + +
99F PHE* 3.4 38.9 - + + -
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Residues in contact with LEU 137 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967 LEU* 4.9 8.3 - - + -
1087 LEU* 4.3 34.8 - - + -
1127 LEU* 5.3 9.2 - - + -
1337 ILE* 3.1 32.8 + - + +
1347 HIS* 3.3 11.7 - - - +
1367 TRP* 1.4 90.0 - - + +
1387 THR* 1.3 62.9 + - - +
1407 ALA* 3.1 22.1 + - - +
1417 MET* 3.3 23.6 + - + +
1557 MET* 4.8 9.0 - - - -
1577 ILE* 4.2 26.0 - - + -
1707 VAL* 4.8 12.8 - - + -
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Residues in contact with THR 138 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906 LEU* 5.4 9.0 - - + -
1347 HIS* 2.8 20.4 + - - -
1357 SER* 3.0 10.7 + - - -
1377 LEU* 1.3 76.7 - - - +
1397 ARG* 1.4 79.1 + - - +
1417 MET* 3.5 11.3 + - - +
1427 TYR* 3.2 22.4 + - + +
1707 VAL* 3.9 12.7 - - + +
1747 GLY* 3.7 23.0 - - - +
1767 ALA* 4.0 19.7 - - + +
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Residues in contact with ARG 139 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876 GLY* 5.2 1.0 + - - -
906 LEU* 5.4 10.0 - - - +
916 THR* 4.0 14.0 + - - +
1357 SER* 3.1 19.5 + - - +
1367 TRP* 3.5 10.1 - - + +
1387 THR* 1.4 100.9 + - - +
1407 ALA* 1.3 56.8 + - - +
1427 TYR* 3.1 55.3 + - - +
1437 SER* 3.0 33.7 + - - -
97F PHE* 3.6 47.3 - - + -
98F VAL* 4.5 21.8 - - + +
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Residues in contact with ALA 140 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087 LEU* 5.8 5.8 - - + -
1367 TRP* 3.4 24.5 + - + +
1377 LEU* 3.1 17.4 + - - +
1397 ARG* 1.3 76.5 - - - +
1417 MET* 1.3 64.7 + - + +
1427 TYR 3.4 0.5 + - - -
1437 SER* 3.5 11.1 + - - -
1447 ARG* 3.4 20.0 + - - +
1517 LEU* 5.1 4.5 - - + -
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Residues in contact with MET 141 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087 LEU* 6.2 1.8 - - + -
1377 LEU* 3.5 27.1 - - + +
1387 THR* 3.8 11.4 - - - +
1397 ARG 3.4 0.2 - - - -
1407 ALA* 1.3 76.3 - - + +
1427 TYR* 1.4 61.6 + - - +
1447 ARG* 3.2 5.1 + - - +
1457 ARG* 3.1 25.3 + - + +
1517 LEU* 3.9 28.5 - - - -
1537 ASN* 5.4 6.5 - - + +
1557 MET* 4.5 23.3 - - + -
1707 VAL* 3.9 31.2 - - + -
1717 ASP 3.9 23.1 - - - +
1727 MET* 5.1 7.0 - - - +
1747 GLY* 4.5 12.8 - - - -
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Residues in contact with TYR 142 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876 GLY* 3.4 29.3 + - - -
886 ASP* 3.7 16.8 + - - -
916 THR* 3.2 34.6 + - + +
1276 ARG* 3.9 10.0 + - - -
1306 PHE* 6.0 3.8 - + - -
1387 THR 3.2 11.0 + - - +
1397 ARG* 3.1 40.6 + - - +
1417 MET* 1.4 77.0 - - - +
1437 SER* 1.4 57.6 - - - +
1457 ARG* 3.5 19.3 + - + +
1467 SER* 2.7 41.2 + - - -
1737 LEU 6.1 0.9 - - - -
1747 GLY* 6.0 4.7 - - - -
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Residues in contact with SER 143 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1397 ARG 3.0 13.9 + - - -
1407 ALA* 3.7 9.9 + - - -
1427 TYR* 1.4 81.2 - - - +
1447 ARG* 1.4 64.0 + - - +
1467 SER* 3.3 10.1 - - - -
1477 LYS* 3.1 30.4 + - - +
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Residues in contact with ARG 144 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221 TYR* 4.8 12.7 + - - -
477 GLN* 3.4 16.3 + - - +
1047 ASP* 5.1 1.0 + - - -
1407 ALA 3.4 15.9 + - - +
1417 MET* 3.2 8.2 + - - +
1437 SER* 1.4 78.9 - - - +
1457 ARG* 1.3 57.9 - - - +
1477 LYS* 3.1 21.3 + - - +
1487 MET 2.9 22.0 + - - -
1497 ASN* 3.1 33.5 + - - +
1507 PRO* 3.1 26.1 + - + -
1517 LEU* 3.7 39.7 - - + +
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Residues in contact with ARG 145 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296 ARG* 5.5 0.4 + - - +
306 PHE* 4.5 11.4 - - + -
316 SER 5.8 1.6 - - - +
346 VAL* 3.9 9.5 - - - +
856 PHE* 3.3 26.7 - - - -
1326 TYR* 3.1 48.2 + - + +
1417 MET 3.1 13.4 + - - +
1427 TYR* 3.5 20.4 - - + +
1447 ARG* 1.3 78.6 - - - +
1467 SER* 1.3 55.0 + - - +
1487 MET* 3.0 31.1 + - - +
1507 PRO* 4.8 9.8 - - + +
1727 MET 3.8 13.0 + - - +
1737 LEU* 2.9 54.9 + - - +
1747 GLY* 5.4 1.1 - - - -
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Residues in contact with SER 146 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306 PHE* 6.0 5.1 - - - -
1427 TYR* 2.7 36.1 + - - -
1437 SER* 3.3 12.2 - - - -
1457 ARG* 1.3 73.0 - - - +
1477 LYS* 1.4 62.1 + - - +
1487 MET* 3.3 14.2 - - - +
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Residues in contact with LYS 147 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437 SER* 3.1 19.6 + - - +
1447 ARG* 3.1 24.7 + - - +
1467 SER* 1.4 75.4 - - - +
1487 MET* 1.4 70.5 + - - +
1497 ASN* 3.9 29.3 - - + +
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Residues in contact with MET 148 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296 ARG* 3.5 41.3 + - - +
326 PRO* 5.7 4.5 - - + -
1316 PRO* 5.3 20.6 - - + -
1326 TYR* 6.5 1.1 - - + -
1447 ARG 2.9 3.8 + - - -
1457 ARG* 3.0 20.8 + - - +
1467 SER* 3.3 21.8 - - - +
1477 LYS* 1.4 80.9 - - - +
1497 ASN* 1.3 64.7 + - - +
1507 PRO* 3.8 5.8 - - - +
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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
------------------------------------------------------------
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