Contacts of the helix formed by residues 112 - 127 (chain 6) 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 THR 112 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106 ALA 3.7 2.9 + - - -
1116 MET* 1.3 78.1 - - - +
1136 THR* 1.3 77.6 + - + +
1146 GLY* 3.8 12.1 - - - +
1156 ALA* 3.3 13.1 + - + +
1166 ILE* 3.3 21.9 + - - +
1426 ASP* 6.0 1.7 - - - -
1436 GLU* 6.0 1.6 - - - +
105E GLU* 4.5 15.9 + - - +
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Residues in contact with THR 113 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786 THR* 5.6 7.2 - - - +
1126 THR* 1.3 85.1 + - + +
1146 GLY* 1.4 59.4 + - - +
1166 ILE* 3.3 14.9 + - - +
1176 ALA* 2.9 27.3 + - - +
1386 ILE* 3.7 12.6 - - - +
1396 GLY 5.1 1.7 - - - -
1406 GLY* 5.1 6.9 + - - -
1416 LEU 5.6 5.8 - - - +
1426 ASP* 3.6 26.2 - - - +
1486 ALA* 4.2 10.4 + - + -
1506 TYR* 4.2 27.4 - - + +
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Residues in contact with GLY 114 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126 THR* 3.2 7.3 - - - +
1136 THR* 1.4 67.7 - - - +
1156 ALA* 1.4 58.9 + - - +
1176 ALA* 3.0 23.3 + - - +
1186 ALA* 3.1 13.5 + - - +
1506 TYR* 5.0 6.3 - - - -
103E TYR 5.4 3.3 - - - +
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Residues in contact with ALA 115 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036 TYR* 6.4 0.2 - - + -
1116 MET* 3.9 12.1 - - + -
1126 THR* 3.3 28.5 + - + +
1136 THR 3.3 0.4 - - - -
1146 GLY* 1.4 73.0 - - - +
1166 ILE* 1.3 57.9 - - - +
1186 ALA* 3.5 2.4 + - - +
1196 MET* 3.1 22.2 + - - +
103E TYR* 3.3 41.4 + - + +
105E GLU* 3.9 16.8 - - - +
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Residues in contact with ILE 116 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746 LEU* 4.7 14.8 - - + -
786 THR* 4.1 27.6 - - + +
806 ILE* 5.9 0.2 - - + -
966 ILE* 5.2 8.5 - - + -
1006 LEU* 4.5 13.2 - - + -
1116 MET* 4.0 19.3 - - + +
1126 THR 3.3 17.0 + - - +
1136 THR* 3.5 13.0 - - - +
1156 ALA* 1.3 75.3 - - - +
1176 ALA* 1.4 65.1 + - - +
1196 MET* 3.1 11.7 + - + +
1206 LEU* 3.0 41.0 + - + +
1386 ILE* 4.3 12.8 - - + -
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Residues in contact with ALA 117 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136 THR 2.9 14.2 + - - +
1146 GLY* 3.0 16.7 + - - +
1166 ILE* 1.4 77.3 - - - +
1186 ALA* 1.4 58.8 + - - +
1206 LEU* 3.5 9.5 + - - +
1216 SER* 3.2 16.5 + - - -
1386 ILE* 3.7 19.3 - - + -
1506 TYR* 4.4 12.3 - - + -
1526 PHE* 3.8 18.4 - - + -
1586 TYR* 5.5 7.6 - - + -
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Residues in contact with ALA 118 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146 GLY 3.1 10.5 + - - +
1156 ALA 3.7 7.0 - - - +
1176 ALA* 1.4 70.3 - - - +
1196 MET* 1.4 66.8 + - - +
1216 SER* 3.2 19.4 + - - -
1226 THR* 3.4 18.5 - - + +
1586 TYR* 6.5 0.7 - - - -
101E PHE 5.4 1.8 - - - +
102E THR 3.0 27.4 - - - +
103E TYR* 4.5 6.1 - - - -
104E ASN* 5.5 4.7 - - - +
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Residues in contact with MET 119 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966 ILE* 3.7 48.7 - - + +
996 ARG* 3.8 40.4 - - + +
1006 LEU* 5.4 1.1 - - + -
1116 MET* 3.9 24.5 - - - +
1156 ALA 3.1 14.9 + - - +
1166 ILE* 3.1 15.0 + - + +
1186 ALA* 1.4 75.7 - - - +
1206 LEU* 1.4 60.4 + - + +
1226 THR* 2.6 27.3 + - - +
1236 ILE* 3.2 19.5 - - + +
102E THR* 5.4 3.4 - - + -
103E TYR* 4.4 12.8 - - + +
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Residues in contact with LEU 120 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806 ILE* 4.8 6.3 - - + -
826 CYS* 5.7 2.0 - - - -
926 LEU* 5.9 4.5 - - + -
966 ILE* 3.6 33.4 - - + -
1166 ILE* 3.0 23.0 + - + +
1176 ALA 3.7 3.8 - - - +
1196 MET* 1.4 73.8 - - + +
1216 SER* 1.4 63.3 + - - +
1236 ILE* 3.2 23.6 + - + +
1246 LEU* 3.2 18.3 + - + +
1366 ASN* 4.7 19.7 - - + +
1386 ILE* 3.7 21.1 - - + -
1526 PHE* 3.5 41.1 - - + -
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Residues in contact with SER 121 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135 PHE* 3.5 22.5 - - - -
1176 ALA 3.2 14.0 + - - -
1186 ALA* 3.2 11.8 + - - -
1206 LEU* 1.4 76.4 - - - +
1226 THR* 1.3 60.2 + - - +
1246 LEU* 3.2 11.8 + - - +
1256 TYR* 2.9 30.3 + - - +
1526 PHE* 4.6 10.3 - - - -
1566 GLY* 4.5 9.2 - - - -
1576 SER 4.8 5.1 + - - -
1586 TYR* 5.0 9.0 - - - -
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Residues in contact with THR 122 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135 PHE* 3.9 23.6 - - + -
1165 ARG* 5.4 3.6 - - - +
996 ARG* 5.4 1.2 + - - -
1186 ALA* 3.4 16.2 - - + +
1196 MET* 2.6 24.8 + - - +
1216 SER* 1.3 72.7 - - - +
1236 ILE* 1.4 66.7 + - - +
1256 TYR* 3.4 2.6 + - - +
1266 SER* 3.1 27.0 + - - -
101E PHE* 5.9 4.0 - - + -
102E THR* 5.4 15.9 - - + +
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Residues in contact with ILE 123 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926 LEU* 4.0 28.7 - - + -
956 ILE* 5.2 6.3 - - + -
966 ILE* 5.0 5.6 - - + -
996 ARG* 3.7 31.4 - - - +
1196 MET* 3.2 31.2 - - + +
1206 LEU* 3.3 21.3 - - + +
1216 SER 3.2 0.4 - - - -
1226 THR* 1.4 83.4 + - - +
1246 LEU* 1.4 58.6 + - + +
1266 SER* 3.4 8.7 + - - -
1276 ARG* 3.1 35.7 + - + +
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Residues in contact with LEU 124 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926 LEU* 5.0 5.4 - - + -
1206 LEU 3.4 19.3 - - - +
1216 SER* 3.2 7.7 + - - +
1236 ILE* 1.4 79.8 - - + +
1256 TYR* 1.3 63.7 + - - +
1276 ARG* 3.0 19.3 + - + +
1286 ARG* 3.0 21.5 + - - +
1336 TYR* 5.3 6.2 - - + -
1346 VAL* 4.7 15.5 - - + +
1366 ASN* 3.7 30.5 - - - +
1526 PHE* 4.3 12.3 - - + -
1536 ASP 3.8 21.8 - - - +
1546 PRO* 5.2 3.6 - - + -
1556 VAL* 3.9 9.1 - - - +
1566 GLY* 4.0 18.2 - - - +
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Residues in contact with TYR 125 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095 ALA* 3.6 19.5 - - + -
1105 ASP* 3.5 13.5 - - - -
1135 PHE* 3.3 59.8 - + + +
1145 TRP* 2.8 54.9 + + - -
1545 LEU* 5.6 4.5 - - + -
1216 SER 2.9 15.7 + - - +
1226 THR 3.7 5.4 - - - +
1246 LEU* 1.3 74.4 - - - +
1266 SER* 1.4 56.6 + - - +
1286 ARG* 3.1 28.0 - - + +
1296 PHE* 4.9 4.7 - - - -
1556 VAL 3.9 14.8 + - - -
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Residues in contact with SER 126 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226 THR 3.1 14.7 + - - -
1236 ILE* 3.5 11.2 - - - -
1246 LEU 3.2 0.2 - - - -
1256 TYR* 1.4 68.8 - - - +
1276 ARG* 1.4 60.8 + - - +
1286 ARG 3.1 6.4 + - - -
1296 PHE* 3.5 23.5 + - - +
1306 PHE* 4.2 11.0 - - - -
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Residues in contact with ARG 127 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886 ASP* 3.1 37.0 + - - +
916 THR* 4.2 13.3 - - - +
926 LEU* 3.6 32.5 - - - +
1236 ILE* 3.1 23.3 + - + +
1246 LEU* 3.0 24.7 + - + +
1266 SER* 1.4 72.4 - - - +
1286 ARG* 1.4 54.6 + - - +
1296 PHE 3.1 3.8 - - - -
1306 PHE* 2.7 77.6 + - + +
1326 TYR 4.6 8.2 + - - -
1336 TYR* 3.4 15.8 - - + +
1346 VAL* 5.1 3.4 - - - +
1427 TYR* 3.9 15.5 + - - -
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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
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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