Contacts of the helix formed by residues 102 - 115 (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 TYR 102 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1531 MET* 3.2 45.9 - - + +
517 VAL* 3.2 19.0 + - + +
527 THR* 3.8 6.5 - - - -
537 GLY* 3.7 26.7 - - - -
727 LEU 2.9 29.1 + - - -
737 GLY* 4.0 8.5 - - - -
847 ILE* 3.6 17.3 - - + +
857 SER 3.5 18.6 - - - -
867 ARG* 3.1 31.9 + - + +
987 ALA 5.9 1.3 - - - -
1007 GLY 3.2 5.7 + - - -
1017 ASP* 1.3 68.7 + - - +
1037 ALA* 1.3 63.2 + - - +
1047 ASP 3.3 1.3 - - - -
1057 PHE* 3.3 22.6 - + - +
1067 GLN* 3.2 15.2 + - - +
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Residues in contact with ALA 103 (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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1181 LYS* 3.6 8.1 + - - +
1221 TYR* 3.5 23.0 - - + -
1251 ARG* 4.6 3.4 - - - +
1511 GLY* 3.1 35.7 - - - +
1531 MET* 3.9 10.8 - - + +
507 MET* 5.7 1.6 - - + -
517 VAL* 4.7 1.0 + - + +
1017 ASP* 3.0 12.4 + - - +
1027 TYR* 1.3 78.3 - - - +
1047 ASP* 1.4 63.2 + - - +
1067 GLN* 3.5 12.0 + - - +
1077 TYR 3.5 7.1 + - - -
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Residues in contact with ASP 104 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221 TYR* 3.2 25.0 + - - -
1251 ARG* 5.4 1.2 + - - -
477 GLN* 4.6 5.6 + - - +
1017 ASP* 3.3 19.8 + - - +
1027 TYR 3.3 0.4 - - - -
1037 ALA* 1.4 73.9 - - - +
1057 PHE* 1.3 64.1 + - - +
1077 TYR* 3.1 14.6 + - - +
1087 LEU* 3.1 14.7 + - - +
1447 ARG* 5.1 1.1 + - - -
1517 LEU* 3.5 25.5 - - + +
1527 TRP* 3.3 24.0 + - - +
1537 ASN* 3.3 20.9 - - - +
1557 MET* 5.8 0.9 - - - -
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Residues in contact with PHE 105 (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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1531 MET* 6.3 0.7 - - + -
857 SER 5.0 2.0 - - - -
867 ARG* 3.7 36.6 - - - -
877 ILE 4.6 0.9 - - - -
887 MET* 4.0 14.4 - - + -
967 LEU* 4.3 17.9 - - + -
987 ALA* 3.4 29.2 - - + -
1017 ASP 3.2 10.8 + - - +
1027 TYR* 3.3 28.5 - + - +
1047 ASP* 1.3 77.6 - - - +
1067 GLN* 1.4 65.8 + - + +
1077 TYR 3.2 0.2 + - - -
1087 LEU* 3.3 7.6 + - + +
1097 LYS* 3.0 59.9 + - + +
1537 ASN* 4.2 7.4 - - - +
1557 MET* 4.7 8.7 - - + -
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Residues in contact with GLN 106 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181 LYS* 3.5 27.4 + - - -
1521 GLY 3.9 5.0 - - - +
1531 MET* 3.4 26.5 - - + +
1541 MET* 3.4 50.4 + - + +
1027 TYR 3.2 3.9 + - - +
1037 ALA 3.5 10.1 - - - +
1047 ASP 3.3 0.4 - - - -
1057 PHE* 1.4 81.0 - - + +
1077 TYR* 1.4 63.1 + - - +
1097 LYS* 3.5 38.7 + - + +
1107 GLN* 3.6 14.2 + - - +
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Residues in contact with TYR 107 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181 LYS* 3.8 13.2 - - - -
1191 GLU* 3.7 37.4 + - - +
1221 TYR* 3.5 57.7 - + + +
1231 ARG* 5.2 2.6 + - - +
1037 ALA 3.5 4.0 + - - +
1047 ASP* 3.1 15.1 + - - +
1067 GLN* 1.4 77.9 - - - +
1087 LEU* 1.3 61.8 + - - +
1107 GLN* 3.2 32.2 + - - +
1117 VAL* 3.6 13.9 - - - +
1517 LEU* 6.3 1.6 - - + -
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Residues in contact with LEU 108 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967 LEU* 3.8 28.7 - - + -
1047 ASP 3.1 8.3 + - - +
1057 PHE* 3.5 13.7 - - + +
1077 TYR* 1.3 78.3 - - - +
1097 LYS* 1.3 68.2 + - - +
1107 GLN 3.2 0.4 - - - -
1117 VAL* 3.3 10.4 + - + -
1127 LEU* 3.2 25.6 + - + +
1367 TRP* 4.7 15.5 - - + -
1377 LEU* 4.3 20.9 - - + -
1407 ALA* 5.8 5.6 - - + -
1417 MET* 6.2 2.2 - - + -
1517 LEU* 6.4 1.8 - - + -
1557 MET* 3.9 23.8 - - + -
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Residues in contact with LYS 109 (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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1531 MET* 5.9 3.0 - - - +
857 SER* 5.1 8.3 + - - -
877 ILE 5.5 4.0 + - - -
887 MET* 4.5 27.3 - - + +
1057 PHE* 3.0 57.8 + - + +
1067 GLN* 3.6 31.9 - - + +
1077 TYR 3.4 0.6 - - - -
1087 LEU* 1.3 78.3 - - + +
1107 GLN* 1.3 58.0 + - + +
1127 LEU* 3.2 11.1 - - - +
1137 GLY* 3.0 23.7 + - - -
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Residues in contact with GLN 110 (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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1181 LYS* 6.0 0.9 - - - +
1191 GLU* 4.7 14.1 + - - +
1067 GLN 3.7 9.0 - - - +
1077 TYR* 3.2 42.8 + - - +
1087 LEU 3.2 0.8 - - - -
1097 LYS* 1.3 75.8 - - + +
1117 VAL* 1.4 68.6 + - + +
1137 GLY* 3.0 4.8 + - - +
1147 GLN* 3.0 21.0 + - - +
101G SER* 4.1 37.4 + - - +
102G ASN* 5.5 1.4 - - - -
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Residues in contact with VAL 111 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077 TYR* 3.6 19.1 - - + +
1087 LEU* 3.3 12.0 + - + +
1107 GLN* 1.4 75.5 - - + +
1127 LEU* 1.3 63.7 + - - +
1147 GLN* 3.0 27.9 + - - +
1157 MET* 3.5 28.9 + - + +
1367 TRP* 4.1 16.4 - - + -
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Residues in contact with LEU 112 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887 MET* 3.8 30.5 - - + -
907 VAL* 3.9 38.6 - - + -
967 LEU* 4.3 12.8 - - + -
1087 LEU* 3.2 15.3 + - + +
1097 LYS* 3.2 10.8 - - - +
1117 VAL* 1.3 76.3 - - - +
1137 GLY* 1.4 60.2 + - - +
1157 MET* 3.1 36.6 + - + +
1167 VAL* 4.1 3.5 + - - +
1247 ASP* 4.3 6.7 - - - +
1337 ILE* 4.9 14.4 - - + -
1367 TRP* 5.6 8.0 - - + -
1377 LEU* 5.3 10.5 - - + -
1577 ILE* 6.2 0.4 - - + -
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Residues in contact with GLY 113 (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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887 MET* 5.5 4.9 - - - -
1097 LYS 3.0 13.4 + - - -
1107 GLN* 3.0 7.1 + - - -
1127 LEU* 1.4 73.1 - - - +
1147 GLN* 1.4 62.7 + - - +
1157 MET 3.3 0.5 + - - -
1167 VAL* 3.7 13.6 + - - +
1177 ILE* 3.7 20.3 - - - +
101G SER* 5.9 0.7 - - - -
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Residues in contact with GLN 114 (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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1107 GLN 3.0 10.3 + - - +
1117 VAL* 3.0 21.5 + - - +
1137 GLY* 1.4 75.3 - - - +
1157 MET* 1.4 65.0 + - - +
1167 VAL 3.2 1.7 + - - -
1177 ILE* 3.3 22.8 + - + +
1187 ASP* 3.2 34.6 + - - +
94G GLU* 5.1 9.8 + - - +
97G SER* 4.2 17.6 + - - -
98G ASN* 3.5 24.5 + - - +
101G SER* 5.3 7.9 + - - +
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Residues in contact with MET 115 (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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1117 VAL* 3.6 21.3 - - + +
1127 LEU* 3.1 27.4 + - + +
1147 GLN* 1.4 80.1 - - - +
1167 VAL* 1.4 57.6 + - - +
1187 ASP* 4.4 5.3 + - - +
1197 GLU* 5.0 0.5 - - - +
1237 GLY* 3.0 24.7 - - - +
1247 ASP* 3.4 18.6 - - - +
1287 TYR* 4.7 22.6 - - + -
1367 TRP* 3.5 53.4 - - + +
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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