Contacts of the helix formed by residues 112 - 127 (chain 3) in PDB entry 1MVW
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 PRO 112 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753 ILE* 3.9 16.4 - - + -
1103 LEU 3.3 8.3 - - - +
1113 ASN* 1.3 95.1 - - - +
1133 LYS* 1.3 57.0 + - - +
1143 ALA* 3.0 4.9 - - + +
1153 ASN* 2.8 48.5 + - - +
1163 ARG* 3.5 4.2 + - - +
1944 THR 6.0 0.2 - - - +
1954 GLU* 4.5 30.5 - - + +
1974 GLY* 6.4 0.9 - - - -
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Residues in contact with LYS 113 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113 ASN 3.4 5.0 + - - -
1123 PRO* 1.3 69.4 - - - +
1143 ALA* 1.3 56.4 - - - +
1163 ARG* 3.4 3.4 + - - +
1173 GLU* 3.1 37.1 + - - +
3713 HIS* 3.2 45.1 + - + +
2564 ARG* 6.1 0.8 - - - +
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Residues in contact with ALA 114 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 PRO* 4.5 4.7 - - + +
1133 LYS* 1.3 78.6 - - - +
1153 ASN* 1.3 63.2 + - - +
1173 GLU* 3.7 14.2 - - - +
1183 LYS* 3.0 25.3 + - - +
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Residues in contact with ASN 115 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753 ILE* 3.5 24.4 - - - +
763 ILE* 3.8 15.9 + - + +
793 TRP* 3.6 26.9 + - + -
1113 ASN* 3.3 26.6 + - - +
1123 PRO* 2.8 26.4 + - - +
1143 ALA* 1.3 72.9 - - - +
1163 ARG* 1.4 59.0 + - - +
1183 LYS* 2.9 3.8 + - - +
1193 MET* 2.8 36.1 + - - +
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Residues in contact with ARG 116 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073 GLU* 3.1 42.4 + - - +
1113 ASN* 4.1 2.1 - - - +
1123 PRO 3.5 2.8 + - - +
1133 LYS* 3.4 11.5 + - - +
1153 ASN* 1.4 76.9 - - - +
1173 GLU* 1.3 57.2 + - - +
1193 MET* 3.4 11.7 - - - +
1203 THR* 2.6 33.0 + - - +
1343 VAL* 3.2 39.5 + - + +
1363 ILE* 4.0 20.2 - - - +
3703 VAL* 3.5 19.7 + - + +
3713 HIS* 3.7 38.6 + - + +
3723 ARG* 3.6 32.1 - - - +
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Residues in contact with GLU 117 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133 LYS* 3.1 21.4 + - - +
1143 ALA* 3.7 14.2 - - - +
1163 ARG* 1.3 76.9 - - - +
1183 LYS* 1.3 54.7 + - - +
1203 THR* 3.4 5.2 + - - -
1213 GLN* 3.0 26.9 + - - +
3673 PRO* 3.6 26.7 - - + +
3683 SER* 3.9 18.7 + - - -
3713 HIS* 3.7 35.0 - - + +
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Residues in contact with LYS 118 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793 TRP* 3.8 45.6 - - + +
1143 ALA 3.0 15.3 + - - +
1153 ASN 2.9 14.2 + - - +
1173 GLU* 1.3 71.7 - - - +
1193 MET* 1.3 55.6 + - - +
1203 THR 3.0 0.2 - - - -
1213 GLN* 3.1 38.8 + - + +
1223 ILE* 3.0 39.2 + - + +
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Residues in contact with MET 119 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123 ASN* 4.8 2.9 - - - +
763 ILE* 4.5 13.9 - - + -
793 TRP* 3.8 10.2 - - + -
863 TRP* 3.9 26.0 - - + -
1053 LEU* 3.7 29.8 - - + -
1063 THR 4.1 19.3 - - - +
1073 GLU* 5.0 0.9 - - + -
1113 ASN* 4.5 11.2 - - - -
1153 ASN* 2.8 19.8 + - - +
1163 ARG* 3.4 20.4 - - - +
1183 LYS* 1.3 71.2 - - - +
1203 THR* 1.3 61.1 + - - +
1223 ILE* 3.8 7.9 - - - +
1233 MET* 2.9 35.0 + - - +
1323 MET* 4.5 0.4 - - - -
1343 VAL* 4.3 16.6 - - + -
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Residues in contact with THR 120 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1163 ARG 2.6 23.2 + - - -
1173 GLU* 3.4 6.7 - - - +
1183 LYS 3.0 0.2 - - - -
1193 MET* 1.3 76.5 - - - +
1213 GLN* 1.3 66.5 - - - +
1243 PHE* 2.9 51.3 + - + +
1323 MET* 3.8 18.0 - - - +
1343 VAL* 4.5 1.7 - - - +
3623 TYR* 4.3 14.4 - - + -
3673 PRO 4.6 2.2 - - - +
3703 VAL* 3.2 33.3 - - + +
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Residues in contact with GLN 121 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173 GLU 3.0 14.3 + - - +
1183 LYS* 3.1 46.9 + - + +
1203 THR* 1.3 75.2 - - - +
1223 ILE* 1.3 63.7 + - - +
1253 GLU* 2.8 65.7 + - - +
1263 THR* 4.9 7.5 - - - +
3623 TYR* 3.6 18.1 + - - +
3673 PRO* 4.7 6.7 - - + +
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Residues in contact with ILE 122 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793 TRP* 3.6 41.5 - - + +
833 GLU* 4.1 18.2 - - + +
863 TRP* 4.1 14.8 - - + -
1183 LYS* 3.0 30.7 + - - +
1193 MET* 4.1 5.6 - - - +
1213 GLN* 1.3 90.6 - - - +
1233 MET* 1.3 68.5 + - - +
1263 THR* 2.9 42.6 + - + +
1273 PHE* 3.2 19.8 + - + -
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Residues in contact with MET 123 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863 TRP* 3.3 55.9 - - + +
903 PHE* 4.1 17.7 - - + -
1033 THR* 4.6 9.0 - - - -
1053 LEU* 3.7 14.8 - - + -
1193 MET 2.9 23.3 + - - +
1203 THR 3.2 1.3 + - - +
1223 ILE* 1.3 80.3 - - - +
1243 PHE* 1.3 59.1 + - - +
1273 PHE* 3.2 24.1 + - + +
1283 ASN 3.0 21.0 + - - -
1293 VAL* 3.6 21.5 + - + +
1323 MET* 3.6 28.5 - - + -
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Residues in contact with PHE 124 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203 THR* 2.9 28.7 + - + +
1233 MET* 1.3 78.7 - - - +
1253 GLU* 1.3 59.4 + - - +
1283 ASN* 3.3 23.4 - - - +
1293 VAL* 3.5 26.9 - - + +
1303 PRO 3.7 10.8 - - - -
1313 ALA* 3.8 5.2 - - - -
1323 MET* 3.4 27.4 - - + -
3573 ILE* 3.0 47.6 - - + -
3583 THR 4.0 2.7 - - - -
3593 LYS* 3.8 13.7 - - + -
3623 TYR* 3.6 37.7 - + + -
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Residues in contact with GLU 125 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213 GLN* 2.8 49.2 + - - +
1243 PHE* 1.3 75.4 - - - +
1263 THR* 1.4 58.1 + - + +
1283 ASN* 4.7 1.7 - - - +
3623 TYR* 3.5 33.1 + - + -
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Residues in contact with THR 126 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833 GLU* 4.2 25.4 + - - +
1213 GLN* 4.9 9.6 - - - +
1223 ILE* 2.9 37.9 + - + +
1253 GLU* 1.4 78.9 - - + +
1273 PHE* 1.3 72.1 + - - +
1283 ASN* 3.6 2.6 - - - +
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Residues in contact with PHE 127 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833 GLU* 3.7 22.2 - - + -
863 TRP* 3.6 30.3 - + + -
873 HIS* 4.0 20.2 - - + -
903 PHE* 3.6 29.2 - + + -
913 TYR* 4.9 6.9 + + - -
983 PRO* 3.7 19.2 - - + +
993 GLU* 3.5 12.1 + - - +
1223 ILE* 3.4 35.9 - - + -
1233 MET* 3.2 28.8 + - + +
1263 THR* 1.3 83.3 + - - +
1283 ASN* 1.3 72.9 - - - +
1293 VAL* 3.4 9.3 + - + -
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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