Contacts of the helix formed by residues 112 - 127 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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759 ILE* 3.9 16.4 - - + -
1109 LEU 3.3 9.6 - - - +
1119 ASN* 1.3 94.0 - - - +
1139 LYS* 1.3 56.7 + - - +
1149 ALA* 3.0 6.3 - - + +
1159 ASN* 2.8 47.5 + - - +
1169 ARG* 3.5 3.8 + - - +
195V GLU* 5.3 19.1 - - + +
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Residues in contact with LYS 113 (chain 9).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1119 ASN 3.4 4.8 + - - -
1129 PRO* 1.3 70.1 - - - +
1149 ALA* 1.3 56.3 + - - +
1169 ARG* 3.4 4.0 + - - +
1179 GLU* 3.1 36.2 + - - +
3719 HIS* 3.2 46.1 + - + +
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Residues in contact with ALA 114 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129 PRO* 2.9 5.1 + - + +
1139 LYS* 1.3 79.1 - - - +
1159 ASN* 1.3 62.8 + - - +
1179 GLU* 3.7 14.5 - - - +
1189 LYS* 3.0 25.1 + - - +
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Residues in contact with ASN 115 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759 ILE* 3.5 23.8 - - - +
769 ILE* 3.8 16.9 + - + +
799 TRP* 3.6 26.7 + - + -
1119 ASN* 3.3 25.7 + - - +
1129 PRO* 2.8 27.3 + - - +
1149 ALA* 1.3 72.6 - - - +
1169 ARG* 1.4 56.7 + - - +
1179 GLU 3.2 0.2 - - - -
1189 LYS* 2.9 3.6 + - - +
1199 MET* 2.8 36.4 + - - +
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Residues in contact with ARG 116 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079 GLU* 3.1 43.5 + - - +
1119 ASN* 4.1 1.9 - - - +
1129 PRO 3.5 3.2 + - - +
1139 LYS* 3.4 11.9 + - - +
1159 ASN* 1.4 76.9 - - - +
1179 GLU* 1.3 56.8 + - - +
1199 MET* 3.4 12.1 - - - +
1209 THR* 2.6 32.7 + - - +
1349 VAL* 3.2 39.8 + - + +
1359 ALA* 4.9 0.2 - - - +
1369 ILE* 4.0 20.0 - - - +
3709 VAL* 3.5 19.7 + - + +
3719 HIS* 3.7 36.2 + - - +
3729 ARG* 3.6 31.9 - - - +
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Residues in contact with GLU 117 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139 LYS* 3.1 21.0 + - - +
1149 ALA* 3.7 12.7 - - - +
1169 ARG* 1.3 76.4 - - - +
1189 LYS* 1.3 56.0 + - - +
1209 THR* 3.4 5.1 + - - -
1219 GLN* 3.0 26.9 + - - +
3679 PRO* 3.6 27.3 - - + +
3689 SER* 3.9 18.9 + - - -
3719 HIS* 3.7 34.7 - - + +
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Residues in contact with LYS 118 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799 TRP* 3.8 46.1 - - + +
1149 ALA 3.0 16.1 + - - +
1159 ASN 2.9 13.2 + - - +
1179 GLU* 1.3 71.5 - - - +
1199 MET* 1.3 56.4 + - - +
1219 GLN* 3.1 36.3 + - + +
1229 ILE* 3.0 39.0 + - + +
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Residues in contact with MET 119 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129 ASN* 4.8 2.5 - - - +
769 ILE* 4.5 14.4 - - + -
799 TRP* 3.8 9.5 - - + -
869 TRP* 3.9 27.1 - - + -
1059 LEU* 3.7 28.9 - - + -
1069 THR 4.1 20.0 - - - +
1079 GLU* 5.0 0.7 - - + -
1119 ASN* 4.5 11.7 - - - -
1159 ASN 2.8 19.6 + - - +
1169 ARG* 3.4 21.1 - - - +
1189 LYS* 1.3 71.4 - - - +
1209 THR* 1.3 61.3 + - - +
1229 ILE* 3.8 7.5 - - - +
1239 MET* 2.9 35.2 + - - +
1329 MET* 4.5 0.2 - - - -
1349 VAL* 4.3 16.4 - - + -
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Residues in contact with THR 120 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169 ARG 2.6 22.8 + - - -
1179 GLU* 3.4 6.0 + - - -
1189 LYS 3.0 0.2 - - - -
1199 MET* 1.3 76.6 - - - +
1219 GLN* 1.3 66.6 + - - +
1249 PHE* 2.9 51.1 + - + +
1329 MET* 3.8 18.4 - - - +
1349 VAL* 4.5 1.7 - - - +
3629 TYR* 4.3 15.0 - - + -
3679 PRO* 4.6 2.0 - - + +
3699 ILE* 5.4 0.2 - - + -
3709 VAL* 3.2 33.1 - - + +
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Residues in contact with GLN 121 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179 GLU 3.0 14.6 + - - +
1189 LYS* 3.1 47.3 + - + +
1209 THR* 1.3 75.7 - - - +
1229 ILE* 1.3 63.6 + - - +
1259 GLU* 2.8 65.0 + - - +
1269 THR* 4.9 7.1 - - - +
3629 TYR* 3.6 17.9 + - - +
3679 PRO* 4.7 6.3 - - + +
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Residues in contact with ILE 122 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799 TRP* 3.6 40.4 - - + +
839 GLU* 4.1 20.4 - - + +
869 TRP* 4.1 14.8 - - + -
1189 LYS* 3.0 29.8 + - - +
1199 MET* 4.1 5.2 - - - +
1219 GLN* 1.3 90.9 - - - +
1239 MET* 1.3 69.1 + - - +
1269 THR* 2.9 43.2 + - + +
1279 PHE* 3.2 19.3 + - + -
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Residues in contact with MET 123 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869 TRP* 3.3 55.4 - - + +
909 PHE* 4.1 17.0 - - + -
1039 THR* 4.6 8.5 - - - -
1059 LEU* 3.7 14.6 - - + -
1199 MET 2.9 24.2 + - - +
1209 THR 3.8 1.1 - - - +
1229 ILE* 1.3 80.3 - - - +
1249 PHE* 1.3 58.0 + - - +
1279 PHE* 3.2 25.8 + - + +
1289 ASN 3.0 21.1 + - - -
1299 VAL* 3.6 20.6 + - + -
1329 MET* 3.6 28.5 - - + -
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Residues in contact with PHE 124 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209 THR* 2.9 28.2 + - + +
1239 MET* 1.3 78.3 - - - +
1259 GLU* 1.3 59.4 + - - +
1289 ASN* 3.3 22.9 - - - +
1299 VAL* 3.5 26.7 - - + +
1309 PRO 3.7 10.8 - - - -
1319 ALA* 3.8 5.4 - - - -
1329 MET* 3.4 26.2 - - + -
3579 ILE* 3.0 47.6 - - + -
3589 THR 4.0 2.9 - - - -
3599 LYS* 3.8 15.0 - - + -
3629 TYR* 3.6 38.1 - + + -
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Residues in contact with GLU 125 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219 GLN* 2.8 51.3 + - - +
1249 PHE* 1.3 75.2 - - - +
1269 THR* 1.4 58.5 + - + +
1289 ASN* 4.7 2.0 - - - +
3629 TYR* 3.5 33.1 + - + -
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Residues in contact with THR 126 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839 GLU* 4.2 25.9 + - - +
1219 GLN* 4.9 9.4 - - - +
1229 ILE* 2.9 37.7 + - + +
1259 GLU* 1.4 77.4 - - + +
1279 PHE* 1.3 73.0 + - - +
1289 ASN* 3.6 1.9 - - - +
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Residues in contact with PHE 127 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839 GLU* 3.7 21.8 - - + -
869 TRP* 3.6 32.5 - + + -
879 HIS* 4.0 20.0 - - + -
909 PHE* 3.6 30.5 - + + -
919 TYR* 4.9 7.0 - + - -
989 PRO* 3.7 19.5 - - + +
999 GLU* 3.5 13.4 - - - +
1229 ILE* 3.4 36.8 - - + -
1239 MET* 3.2 27.7 + - + +
1269 THR* 1.3 82.0 + - - +
1289 ASN* 1.3 73.2 + - - +
1299 VAL* 3.4 9.0 + - + -
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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