Contacts of the helix formed by residues 112 - 127 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752 ILE* 3.9 16.4 - - + -
1102 LEU 3.3 10.5 - - - +
1112 ASN* 1.3 93.1 - - - +
1132 LYS* 1.3 56.9 + - - +
1142 ALA* 3.0 7.0 - - + +
1152 ASN* 2.8 48.3 + - - +
1162 ARG* 3.5 4.0 + - - +
1943 THR 5.4 2.0 - - - +
1953 GLU* 3.7 37.0 - - + +
1973 GLY* 5.5 4.3 - - - +
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Residues in contact with LYS 113 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112 ASN 3.4 5.0 + - - -
1122 PRO* 1.3 69.4 - - - +
1142 ALA* 1.3 56.7 + - - +
1162 ARG* 3.4 3.8 + - - +
1172 GLU* 3.1 35.9 + - - +
3712 HIS* 3.2 44.8 + - + +
1953 GLU* 6.1 0.4 - - - +
2563 ARG* 5.5 11.1 - - - +
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Residues in contact with ALA 114 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122 PRO* 2.9 4.7 + - + +
1132 LYS* 1.3 78.5 - - - +
1152 ASN* 1.3 63.8 + - - +
1172 GLU* 3.7 13.9 - - - +
1182 LYS* 3.0 24.9 + - - +
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Residues in contact with ASN 115 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752 ILE* 3.5 24.0 - - - +
762 ILE* 3.8 17.1 + - + +
792 TRP* 3.6 27.4 + - + -
1112 ASN* 3.3 26.0 + - - +
1122 PRO* 2.8 26.7 + - - +
1142 ALA* 1.3 72.7 - - - +
1162 ARG* 1.4 56.6 + - - +
1182 LYS* 2.8 3.3 + - - +
1192 MET* 2.8 36.9 + - - +
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Residues in contact with ARG 116 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072 GLU* 3.1 42.1 + - - +
1112 ASN* 4.1 1.7 - - - +
1122 PRO 3.5 3.3 + - - +
1132 LYS* 3.4 12.2 + - - +
1152 ASN* 1.4 76.6 - - - +
1172 GLU* 1.3 55.7 + - - +
1192 MET* 3.4 12.2 - - - +
1202 THR* 2.6 33.2 + - - +
1342 VAL* 3.2 40.8 + - + +
1352 ALA* 4.9 0.2 - - - +
1362 ILE* 4.0 20.6 - - - +
3702 VAL* 3.5 19.9 + - + +
3712 HIS* 3.7 37.3 + - - +
3722 ARG* 3.6 31.7 - - - +
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Residues in contact with GLU 117 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132 LYS* 3.1 21.9 + - - +
1142 ALA* 3.7 13.6 - - - +
1162 ARG* 1.3 76.7 - - - +
1182 LYS* 1.3 56.1 + - - +
1202 THR* 3.4 5.0 + - - -
1212 GLN* 3.0 27.2 + - - +
3672 PRO* 3.6 25.8 - - + +
3682 SER* 3.9 19.1 + - - -
3702 VAL* 5.2 0.2 - - - -
3712 HIS* 3.7 35.3 - - + +
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Residues in contact with LYS 118 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792 TRP* 3.8 46.1 - - + +
1142 ALA 3.0 15.9 + - - +
1152 ASN 2.8 14.7 + - - +
1172 GLU* 1.3 70.5 - - - +
1192 MET* 1.3 56.2 + - - +
1212 GLN* 3.1 36.9 + - + +
1222 ILE* 3.0 38.3 + - + +
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Residues in contact with MET 119 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122 ASN* 4.8 2.7 - - - +
762 ILE* 4.5 14.4 - - + -
792 TRP* 3.8 9.5 - - + -
862 TRP* 3.9 26.5 - - + -
1052 LEU* 3.7 28.9 - - + -
1062 THR 4.1 19.3 - - - +
1072 GLU* 5.0 0.9 - - + -
1112 ASN* 4.5 11.7 - - - -
1152 ASN 2.8 20.1 + - - +
1162 ARG* 3.4 20.0 - - - +
1182 LYS* 1.3 71.8 - - - +
1202 THR* 1.3 61.7 + - - +
1222 ILE* 3.8 7.7 - - - +
1232 MET* 2.9 34.8 + - - +
1322 MET* 4.5 0.2 - - - -
1342 VAL* 4.3 16.6 - - + -
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Residues in contact with THR 120 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162 ARG 2.6 22.7 + - - -
1172 GLU* 3.4 6.5 + - - -
1192 MET* 1.3 77.9 - - - +
1212 GLN* 1.3 66.4 + - - +
1242 PHE* 2.9 50.9 + - + +
1322 MET* 3.8 18.5 - - - +
1342 VAL* 4.5 1.6 - - - +
3622 TYR* 4.3 13.9 - - + -
3672 PRO* 4.6 2.2 - - + +
3692 ILE* 5.4 0.2 - - + -
3702 VAL* 3.2 34.2 - - + +
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Residues in contact with GLN 121 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1172 GLU 3.0 13.9 + - - +
1182 LYS* 3.1 44.6 + - + +
1202 THR* 1.3 74.9 - - - +
1222 ILE* 1.3 64.4 + - - +
1252 GLU* 2.8 64.6 + - - +
1262 THR* 4.9 6.7 - - - +
3622 TYR* 3.6 18.4 - - - +
3672 PRO* 4.7 6.5 - - + +
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Residues in contact with ILE 122 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792 TRP* 3.6 42.0 - - + +
832 GLU* 4.1 18.2 - - + +
862 TRP* 4.1 15.3 - - + -
1182 LYS* 3.0 31.1 + - - +
1192 MET* 4.1 4.7 - - - +
1212 GLN* 1.3 89.1 - - - +
1232 MET* 1.3 68.6 + - - +
1262 THR* 2.9 43.4 + - + +
1272 PHE* 3.2 19.1 + - + -
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Residues in contact with MET 123 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862 TRP* 3.3 56.1 - - + +
902 PHE* 4.1 17.3 - - + -
1032 THR* 4.6 9.6 - - - -
1052 LEU* 3.7 14.6 - - + -
1192 MET 2.9 24.3 + - - +
1202 THR 3.8 1.1 - - - +
1222 ILE* 1.3 79.9 - - - +
1242 PHE* 1.3 57.5 + - - +
1272 PHE* 3.2 24.6 + - + +
1282 ASN 3.0 21.3 + - - -
1292 VAL* 3.6 20.8 + - + +
1322 MET* 3.6 28.3 - - + -
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Residues in contact with PHE 124 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202 THR* 2.9 28.7 + - + +
1232 MET* 1.3 78.6 - - - +
1252 GLU* 1.3 58.1 + - - +
1282 ASN* 3.3 23.0 - - - +
1292 VAL* 3.5 27.1 - - + +
1302 PRO 3.7 10.3 - - - -
1312 ALA* 3.8 5.2 - - - -
1322 MET* 3.4 27.1 - - + -
3572 ILE* 3.0 48.7 - - + -
3582 THR 4.0 2.7 - - - -
3592 LYS* 3.8 14.4 - - + -
3622 TYR* 3.6 38.4 - + + -
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Residues in contact with GLU 125 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212 GLN* 2.8 50.8 + - - +
1242 PHE* 1.3 75.5 - - - +
1262 THR* 1.3 59.6 + - + +
1282 ASN* 4.7 1.4 - - - +
3622 TYR* 3.5 34.3 + - + -
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Residues in contact with THR 126 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832 GLU* 4.2 25.6 + - - +
1212 GLN* 4.9 9.0 - - - +
1222 ILE* 2.9 38.4 + - + +
1252 GLU* 1.3 79.6 - - + +
1272 PHE* 1.3 71.1 + - - +
1282 ASN* 3.6 2.5 - - - +
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Residues in contact with PHE 127 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832 GLU* 3.7 21.1 - - + -
862 TRP* 3.6 32.8 - + + -
872 HIS* 3.9 20.2 - - + -
902 PHE* 3.6 31.0 - + + -
912 TYR* 4.9 7.6 + + - -
982 PRO* 3.6 18.9 - - + +
992 GLU* 3.5 13.3 + - - +
1222 ILE* 3.4 36.3 - - + -
1232 MET* 3.2 29.0 + - + +
1262 THR* 1.3 81.8 + - - +
1282 ASN* 1.3 73.0 + - - +
1292 VAL* 3.4 8.2 + - + -
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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