Contacts of the helix formed by residues 151 - 159 (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 LYS 151 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98K MET* 4.5 28.4 - - + +
101K PHE* 5.2 0.8 - - - -
102K LYS* 5.4 8.6 - - - +
109K LYS* 4.6 21.7 + - - +
149K ASP* 4.5 0.4 - - - +
150K TYR* 1.3 123.5 - - + +
152K ASN* 1.3 67.7 + - - +
153K ILE* 3.1 6.3 - - - +
154K CYS* 3.3 20.1 + - - +
155K TYR* 3.2 33.7 + - + -
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Residues in contact with ASN 152 (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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140K PHE* 5.6 0.2 - - - -
143K ASP* 6.1 0.6 - - - +
144K VAL* 4.4 15.8 - - + +
149K ASP* 3.3 30.7 + - - +
150K TYR* 3.3 2.1 - - - +
151K LYS* 1.3 79.9 - - - +
153K ILE* 1.3 59.5 + - - +
155K TYR* 3.4 13.6 + - - +
156K VAL* 3.1 36.3 + - + +
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Residues in contact with ILE 153 (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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101K PHE* 5.0 18.2 - - + -
117K LEU* 6.5 0.2 - - + -
140K PHE* 4.0 21.1 - - + -
144K VAL* 2.0 74.9 - - + +
147K ASN* 5.9 0.2 - - - -
149K ASP 5.0 6.5 - - - +
150K TYR* 5.5 2.0 - - - -
151K LYS 5.0 5.4 - - - +
152K ASN* 1.3 75.6 - - - +
154K CYS* 1.3 57.1 + - - +
156K VAL* 3.3 1.7 + - - +
157K ILE* 2.9 52.7 + - + +
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Residues in contact with CYS 154 (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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94K GLU* 3.4 11.6 - - + +
97K ILE* 3.5 40.4 - - + +
98K MET* 3.6 28.0 - - + -
101K PHE* 3.6 21.1 - - - -
150K TYR* 5.6 0.2 - - - -
151K LYS* 3.5 19.5 - - - +
153K ILE* 1.3 75.8 - - - +
155K TYR* 1.3 67.3 + - + +
157K ILE* 3.5 1.7 + - - +
158K THR* 3.2 24.4 + - - -
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Residues in contact with TYR 155 (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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94K GLU* 3.2 28.0 - - - -
98K MET* 5.2 11.2 - - - -
151K LYS* 3.2 20.5 + - + +
152K ASN* 3.4 17.3 - - - +
153K ILE 3.2 0.2 - - - -
154K CYS* 1.3 80.4 - - + +
156K VAL* 1.3 60.7 + - + +
158K THR* 3.0 5.5 + - - -
159K HIS* 2.8 53.7 + + + +
163K ALA* 5.7 6.1 - - + -
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Residues in contact with VAL 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823J PHE* 3.2 22.1 - - + -
140K PHE* 3.6 29.8 - - + -
152K ASN* 3.1 17.7 + - + +
153K ILE 3.3 0.4 + - - -
155K TYR* 1.3 77.3 - - + +
157K ILE* 1.3 61.1 + - - +
158K THR 3.4 0.2 - - - -
159K HIS* 3.0 7.9 - - - +
160K GLY* 3.3 10.5 + - - -
161K GLU 3.7 36.8 - - - +
162K ASP* 5.4 1.8 - - - -
163K ALA* 5.1 11.2 - - + +
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Residues in contact with ILE 157 (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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819J ASN* 4.2 24.9 - - + +
820J VAL* 5.0 17.9 - - + +
823J PHE* 4.1 23.4 - - + +
832J MET* 5.8 1.2 - - - +
836J PHE* 5.0 2.6 - - - -
91K ALA* 6.0 2.0 - - - +
92K ASP 4.4 6.7 + - - +
97K ILE* 3.9 29.8 - - + -
101K PHE* 5.8 1.3 - - + -
140K PHE* 3.9 17.9 - - + -
153K ILE* 2.9 37.8 + - + +
154K CYS 3.9 4.3 - - - +
155K TYR 3.3 0.2 - - - -
156K VAL* 1.3 76.9 - - - +
158K THR* 1.3 60.8 + - - +
159K HIS 4.9 0.2 - - - -
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Residues in contact with THR 158 (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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832J MET* 4.1 9.4 - - - +
835J PHE* 4.6 0.7 - - - -
836J PHE* 3.1 12.1 - - - -
839J MLY 3.0 51.2 + - - -
92K ASP 3.3 19.6 + - - +
93K PRO* 4.9 5.8 - - + -
94K GLU* 3.2 34.7 + - + +
97K ILE* 4.0 0.9 - - - +
154K CYS 3.2 4.4 + - - -
155K TYR 3.0 2.9 + - - -
157K ILE* 1.3 78.9 - - - +
159K HIS* 1.3 59.8 + - - +
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Residues in contact with HIS 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836J PHE* 2.4 21.1 - - + +
839J MLY 3.1 48.0 - - + -
94K GLU* 3.3 16.7 + - - -
155K TYR* 2.8 45.3 + + + +
156K VAL* 3.0 17.9 - - + +
158K THR* 1.3 73.8 - - - +
160K GLY* 1.3 70.2 + - - +
161K GLU 4.2 1.2 + - - +
163K ALA* 5.2 13.1 - - + +
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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