Contacts of the helix formed by residues 129 - 138 (chain K) 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 THR 129 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122K THR* 3.9 7.4 - - - +
125K GLY 4.0 2.1 + - - -
126K GLY* 2.8 31.4 + - - +
127K ARG 3.4 1.4 - - - -
128K PHE* 1.4 83.1 - - - +
130K PRO* 1.4 87.2 - - - +
131K GLU* 3.7 5.5 + - - +
132K GLU* 3.0 24.3 + - - +
133K ILE* 3.0 6.6 + - - +
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Residues in contact with PRO 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K THR* 3.9 16.3 - - + +
129K THR* 1.4 85.4 - - - +
131K GLU* 1.4 50.4 - - - +
132K GLU 2.2 5.1 + - - -
133K ILE* 2.0 59.3 + - + -
134K LYS* 4.3 14.1 - - - +
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Residues in contact with GLU 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K THR* 3.7 5.2 + - - +
130K PRO* 1.4 74.4 - - - +
132K GLU* 1.3 66.9 + - + +
133K ILE 3.1 0.2 - - - -
134K LYS* 3.2 26.1 + - + +
135K ASN* 3.2 36.2 + - - +
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Residues in contact with GLU 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821J ARG* 5.1 9.9 + - - +
121K LEU* 5.9 1.1 - - + -
126K GLY 3.5 2.9 - - - +
127K ARG* 3.3 27.3 - - - +
129K THR* 3.0 36.9 + - - +
130K PRO 2.2 12.0 + - - +
131K GLU* 1.3 78.0 - - + +
133K ILE* 1.3 56.8 + - + +
135K ASN* 3.3 15.7 + - - +
136K MET* 2.9 40.9 + - + +
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Residues in contact with ILE 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K GLU* 3.5 46.9 - - + +
121K LEU* 4.0 16.4 - - + -
122K THR* 3.3 15.7 - - - +
128K PHE 3.0 22.4 - - - +
129K THR 3.0 14.6 - - - +
130K PRO* 2.0 35.4 + - + +
132K GLU 1.3 64.7 - - - -
134K LYS* 1.3 59.4 + - + +
136K MET* 3.2 10.1 + - + +
137K TRP* 3.1 37.2 + - + -
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Residues in contact with LYS 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K PRO* 4.7 10.0 - - + +
131K GLU* 3.2 33.3 + - + +
133K ILE* 1.3 76.3 - - + +
135K ASN* 1.3 61.0 + - - +
137K TRP* 3.3 10.1 + - - +
138K ALA* 3.0 27.9 + - - +
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Residues in contact with ASN 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824J MET* 5.1 20.3 - - + +
827J MLY 5.2 6.0 - - - -
131K GLU* 3.2 32.1 + - - +
132K GLU* 3.5 16.5 - - - +
134K LYS* 1.3 78.2 - - - +
136K MET* 1.3 66.6 + - + +
138K ALA* 3.2 21.6 + - - +
139K ALA 3.8 4.0 + - - -
140K PHE* 5.7 0.3 - - - -
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Residues in contact with MET 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820J VAL* 2.6 46.0 - - + -
824J MET* 4.3 24.9 - - + -
121K LEU* 5.2 13.0 - - + -
127K ARG 5.8 3.1 - - - +
132K GLU* 2.9 34.8 + - + +
133K ILE* 3.2 13.0 + - + +
135K ASN* 1.3 78.9 - - + +
137K TRP* 1.3 59.9 + - + +
138K ALA 3.4 0.3 + - - -
140K PHE* 2.9 49.8 + - + +
145K ALA* 4.2 5.0 - - - +
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Residues in contact with TRP 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K LYS* 3.3 17.9 - - + +
118K GLU* 3.1 27.3 + - - +
133K ILE* 3.1 28.5 + - + +
134K LYS* 3.3 10.3 + - - +
136K MET* 1.3 79.1 - - + +
138K ALA* 1.3 61.6 + - - +
139K ALA 3.4 1.3 + - - -
140K PHE 3.5 11.8 - - - +
141K PRO* 2.8 14.2 - - - +
142K PRO* 1.5 42.0 - - + -
145K ALA* 1.2 84.7 + - + +
146K GLY* 0.8 126.3 - - - -
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Residues in contact with ALA 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K LYS 3.0 16.4 + - - +
135K ASN* 3.4 13.5 - - - +
136K MET 3.2 1.2 - - - -
137K TRP* 1.3 77.7 - - - +
139K ALA* 1.2 65.0 + - + +
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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