Contacts of the helix formed by residues 112 - 127 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751 ILE* 4.0 9.6 - - + -
1101 LEU 3.3 3.1 - - - +
1111 ASN* 1.3 93.5 - - - +
1131 LYS* 1.3 56.3 + - - +
1141 ALA 3.0 3.6 - - - +
1151 ASN* 2.8 38.8 + - - +
1161 ARG* 3.5 3.5 + - - +
1942 THR 3.3 1.8 - - - +
1952 GLU* 1.5 42.1 - - + +
1962 ARG* 2.5 25.6 - - - +
1972 GLY* 2.2 26.9 - - - +
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Residues in contact with LYS 113 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111 ASN 3.4 4.9 + - - -
1121 PRO* 1.3 68.8 - - - +
1141 ALA* 1.3 57.7 + - - +
1161 ARG* 3.4 4.4 + - - +
1171 GLU* 3.1 35.8 + - - +
3711 HIS* 3.2 45.3 + - + +
1952 GLU* 4.7 5.0 - - - +
1962 ARG* 4.9 3.0 - - - +
2272 MET* 6.0 4.5 - - + -
2302 ALA* 6.3 0.7 - - - -
2522 ASN* 3.9 27.3 + - - +
2532 GLU* 3.9 8.1 + - - -
2562 ARG* 3.5 47.5 - - - +
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Residues in contact with ALA 114 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121 PRO* 4.5 1.8 - - + +
1131 LYS* 1.3 79.1 - - - +
1151 ASN* 1.3 62.5 + - - +
1171 GLU* 3.7 13.3 - - - +
1181 LYS* 3.0 24.8 + - - +
1962 ARG* 4.8 27.4 - - + +
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Residues in contact with ASN 115 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751 ILE* 3.5 24.0 - - - +
761 ILE* 3.8 16.9 + - + +
791 TRP* 3.6 26.8 + - + -
1111 ASN* 3.3 25.7 + - - +
1121 PRO* 2.8 26.3 + - - +
1141 ALA* 1.3 72.1 - - - +
1161 ARG* 1.4 57.6 + - - +
1171 GLU 3.2 0.2 - - - -
1181 LYS* 2.9 3.2 + - - +
1191 MET* 2.8 36.9 + - - +
1962 ARG 4.1 6.4 - - - +
1972 GLY* 4.5 2.6 - - - -
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Residues in contact with ARG 116 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071 GLU* 3.1 43.9 + - - +
1111 ASN* 4.1 1.9 - - - +
1121 PRO 3.5 2.5 + - - +
1131 LYS* 3.4 12.0 + - - +
1151 ASN* 1.4 77.9 - - - +
1171 GLU* 1.3 56.0 + - - +
1191 MET* 3.4 12.2 - - - +
1201 THR* 2.6 33.2 + - - +
1341 VAL* 3.2 39.5 + - + +
1361 ILE* 4.0 20.2 - - - +
3701 VAL* 3.5 19.3 + - + +
3711 HIS* 3.7 36.6 + - - +
3721 ARG* 3.6 32.5 - - - +
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Residues in contact with GLU 117 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131 LYS* 3.1 22.6 + - - +
1141 ALA* 3.7 13.1 - - - +
1151 ASN 3.2 0.2 - - - -
1161 ARG* 1.3 77.9 - - - +
1181 LYS* 1.3 54.7 + - - +
1201 THR* 3.4 4.4 + - - -
1211 GLN* 3.0 27.2 + - - +
3671 PRO* 3.6 27.1 - - + +
3681 SER* 3.9 19.3 + - - -
3711 HIS* 3.7 35.2 - - + +
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Residues in contact with LYS 118 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791 TRP* 3.8 45.2 - - + +
1141 ALA 3.0 14.6 + - - +
1151 ASN 2.9 14.8 + - - +
1171 GLU* 1.3 71.5 - - - +
1191 MET* 1.3 56.0 + - - +
1201 THR 3.0 0.2 - - - -
1211 GLN* 3.1 37.0 + - + +
1221 ILE* 3.0 38.4 + - + +
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Residues in contact with MET 119 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121 ASN* 4.8 2.7 - - - +
761 ILE* 4.5 14.6 - - + -
791 TRP* 3.8 10.6 - - + -
861 TRP* 3.9 25.8 - - + -
1051 LEU* 3.7 29.2 - - + -
1061 THR 4.1 19.7 - - - +
1071 GLU* 5.0 0.9 - - + -
1111 ASN* 4.5 11.7 - - - -
1151 ASN* 2.8 19.9 + - - +
1161 ARG* 3.4 20.6 - - - +
1181 LYS* 1.3 71.4 - - - +
1201 THR* 1.3 61.0 + - - +
1221 ILE* 3.8 8.1 - - - +
1231 MET* 2.9 35.0 + - - +
1321 MET* 4.5 0.2 - - - -
1341 VAL* 4.3 16.6 - - + -
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Residues in contact with THR 120 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161 ARG 2.6 22.8 + - - -
1171 GLU* 3.4 6.3 + - - -
1181 LYS 3.0 0.6 - - - -
1191 MET* 1.3 76.5 - - - +
1211 GLN* 1.3 67.2 + - - +
1241 PHE* 2.9 52.1 + - + +
1321 MET* 3.8 17.5 - - - +
1341 VAL* 4.5 2.1 - - - +
3621 TYR* 4.3 14.1 - - + -
3671 PRO* 4.6 2.7 - - + +
3701 VAL* 3.2 33.5 - - + +
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Residues in contact with GLN 121 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171 GLU 3.0 13.5 + - - +
1181 LYS* 3.1 46.1 + - + +
1201 THR* 1.3 75.3 - - - +
1221 ILE* 1.3 63.7 + - - +
1251 GLU* 2.8 64.4 + - - +
1261 THR* 4.9 7.5 - - - +
3621 TYR* 3.6 17.7 + - - +
3671 PRO* 4.7 7.2 - - + +
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Residues in contact with ILE 122 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791 TRP* 3.6 39.7 - - + +
831 GLU* 4.1 19.7 - - + +
861 TRP* 4.1 15.0 - - + -
1181 LYS* 3.0 30.4 + - - +
1191 MET* 4.1 5.2 - - - +
1211 GLN* 1.3 89.1 - - - +
1231 MET* 1.3 68.4 + - - +
1261 THR* 2.9 43.4 + - + +
1271 PHE* 3.2 19.7 + - + -
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Residues in contact with MET 123 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 TRP* 3.3 55.4 - - + +
901 PHE* 4.1 17.7 - - + -
1031 THR* 4.6 9.0 - - - -
1051 LEU* 3.7 15.0 - - + -
1191 MET 2.9 23.8 + - - +
1201 THR 3.2 1.3 + - - +
1221 ILE* 1.3 79.6 - - - +
1241 PHE* 1.3 59.1 + - - +
1271 PHE* 3.2 24.5 + - + +
1281 ASN 3.0 21.1 + - - -
1291 VAL* 3.6 20.3 + - + +
1321 MET* 3.6 27.8 - - + -
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Residues in contact with PHE 124 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1201 THR* 2.9 27.9 + - + +
1231 MET* 1.3 79.1 - - - +
1251 GLU* 1.3 59.5 + - - +
1281 ASN* 3.3 23.2 - - - +
1291 VAL* 3.5 26.5 - - + +
1301 PRO 3.7 11.0 - - - -
1311 ALA* 3.8 4.9 - - - -
1321 MET* 3.4 26.9 - - + -
3571 ILE* 3.0 49.1 - - + -
3581 THR 4.0 2.9 - - - -
3591 LYS* 3.8 13.9 - - + -
3621 TYR* 3.6 38.4 - + + -
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Residues in contact with GLU 125 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211 GLN* 2.8 50.7 + - - +
1241 PHE* 1.3 75.2 - - - +
1261 THR* 1.3 59.4 + - + +
1281 ASN* 4.7 1.6 - - - +
3621 TYR* 3.5 33.4 + - + -
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Residues in contact with THR 126 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831 GLU* 4.2 25.1 + - - +
1211 GLN* 4.9 9.4 - - - +
1221 ILE* 2.9 38.2 + - + +
1251 GLU* 1.3 80.0 - - + +
1271 PHE* 1.3 72.3 + - - +
1281 ASN* 3.6 2.2 - - - +
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Residues in contact with PHE 127 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831 GLU* 3.7 21.3 - - + -
861 TRP* 3.6 31.0 - + + -
871 HIS* 4.0 20.2 - - + -
901 PHE* 3.6 28.3 - + + -
911 TYR* 4.9 7.0 - + - -
981 PRO* 3.7 19.1 - - + +
991 GLU* 3.5 12.8 + - - +
1221 ILE* 3.4 36.3 - - + -
1231 MET* 3.2 29.4 + - + +
1261 THR* 1.3 81.8 + - - +
1281 ASN* 1.3 73.1 + - - +
1291 VAL* 3.3 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