Contacts of the helix formed by residues 13 - 18 (chain J) 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 ALA 13 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10J PHE* 3.2 10.7 + - + +
11J GLY 3.2 0.8 - - - -
12J GLU* 1.3 73.1 - - - +
14J ALA* 1.3 53.7 + - - +
15J PRO* 3.1 5.1 - - - +
16J TYR* 2.6 40.0 + - - +
17J LEU* 3.4 12.5 + - + +
133J PRO* 3.5 34.5 - - + +
134J VAL* 4.6 4.0 - - + -
136J ASN* 5.1 1.7 + - + +
139J VAL* 3.8 22.4 - - + -
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Residues in contact with ALA 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J MET* 3.2 31.3 - - + +
10J PHE* 3.7 7.4 - - + +
11J GLY* 2.8 28.7 + - - +
13J ALA* 1.3 75.6 - - - +
15J PRO* 1.3 55.1 - - + +
17J LEU* 2.9 3.3 + - - -
18J ARG 2.5 40.9 + - - +
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Residues in contact with PRO 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J GLY 3.3 4.0 - - - +
12J GLU 3.2 15.5 - - - +
13J ALA 3.1 6.3 - - - -
14J ALA* 1.3 97.4 - - + +
16J TYR* 1.3 71.6 + - + +
17J LEU 3.4 0.2 - - - -
18J ARG 3.5 12.1 - - - +
19J MLY 3.9 37.3 + - + +
112J ALA 4.2 7.3 - - - +
114J MET* 4.3 3.1 - - - +
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Residues in contact with TYR 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J GLU 4.1 7.2 - - - -
13J ALA 2.6 25.3 + - - +
15J PRO* 1.3 85.8 - - + +
17J LEU* 1.3 61.5 - - - +
112J ALA 4.9 0.4 - - - -
113J TRP* 3.6 42.5 - + + +
114J MET* 3.3 22.4 - - - +
115J ILE* 4.4 4.0 + - - +
116J TYR* 5.5 1.4 + - - -
130J MLY 4.1 23.5 - - - -
131J TRP 5.9 0.4 - - - -
132J LEU* 4.4 13.0 - - + -
133J PRO* 3.2 42.3 - - + +
134J VAL* 4.2 16.6 - - + +
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Residues in contact with LEU 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J MET* 4.4 2.0 - - + -
10J PHE* 3.2 40.4 - - + -
13J ALA* 3.4 20.6 + - + +
14J ALA* 3.5 7.6 - - - +
16J TYR* 1.3 88.9 - - - +
18J ARG* 1.3 60.1 + - - +
109J ARG* 4.2 9.4 + - - -
114J MET* 3.9 13.9 - - - +
116J TYR* 5.2 4.6 - - + +
134J VAL* 4.3 23.1 - - + -
139J VAL* 4.7 4.5 - - + -
143J TYR* 4.0 20.2 - - + +
152J PRO* 3.6 25.2 - - + +
153J PRO* 4.9 12.0 - - - +
154J HIS* 5.0 3.1 - - + +
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Residues in contact with ARG 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J GLU* 3.7 21.4 + - - -
7J MET* 3.3 32.6 - - + +
14J ALA 2.5 28.4 + - - +
15J PRO* 3.5 10.7 - - - +
17J LEU* 1.3 74.6 - - + +
19J MLY 1.3 70.1 + - - +
24J ARG* 4.7 23.7 - - - +
89J GLU* 2.9 40.3 + - - +
109J ARG* 6.0 0.9 - - - +
114J MET* 4.2 6.3 - - + -
149J GLN 4.8 9.1 + - - -
150J GLU 5.1 2.2 + - - -
151J ALA* 4.5 7.7 + - - +
152J PRO* 4.1 21.7 - - + +
719J ASP* 5.1 6.9 + - - -
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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