Contacts of the strand formed by residues 24 - 32 (chain A) in PDB entry 1MM5
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 TYR 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU 4.4 0.2 + - - -
23A HIS* 1.3 68.9 - - - +
25A ASP* 1.3 64.7 + - - +
26A LEU* 4.7 3.0 - - + +
56A PHE* 3.4 48.9 - + + +
57A GLY 4.2 4.0 - - - -
58A LEU* 5.1 16.8 - - + -
160A PHE 4.0 0.3 - - - +
162A PHE* 2.6 50.7 + - + +
163A LEU* 4.4 4.1 - - + +
164A GLU* 4.0 34.1 - - - +
165A HIS* 5.1 5.2 - - + -
166A HIS* 5.0 11.8 + + - -
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A HIS* 3.2 20.1 - - - +
24A TYR* 1.3 75.9 - - - +
26A LEU* 1.3 60.7 + - - +
56A PHE* 3.1 27.5 - - - +
57A GLY 2.9 26.6 + - - +
58A LEU* 4.5 5.8 - - - -
59A SER* 4.8 6.4 + - - -
138A THR* 5.3 4.9 + - - +
159A ARG* 4.1 34.6 + - - +
160A PHE 3.6 12.5 - - - +
161A GLN* 4.1 20.0 - - - +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 4.7 2.5 - - + +
25A ASP* 1.3 77.1 - - - +
27A TYR* 1.3 65.4 + - - +
28A ILE* 5.3 9.4 - - + -
55A GLY 3.0 16.2 - - - +
56A PHE* 3.3 21.5 - - + +
159A ARG* 3.4 4.0 - - - +
160A PHE* 3.0 59.5 + - + +
162A PHE* 4.2 21.5 - - + -
165A HIS* 4.5 18.4 - - + +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 1.3 75.1 - - - +
28A ILE* 1.3 74.8 + - - +
55A GLY* 2.9 34.5 + - - +
56A PHE* 3.0 35.0 + - - -
71A TYR* 4.2 14.0 - + + +
72A ALA 3.9 5.9 + - - -
73A MET* 3.0 40.8 - - + +
85A ILE* 5.8 0.2 - - - +
140A GLN* 4.8 9.0 - - - +
157A TRP* 4.4 28.0 - + + -
158A MET 3.0 18.2 - - - +
159A ARG* 3.6 35.2 - - + -
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 5.3 11.0 - - + -
27A TYR* 1.3 89.9 - - - +
29A PRO* 1.3 103.2 - - + +
52A TRP* 5.9 4.9 - - + -
53A GLY 4.5 8.5 - - - +
54A GLY* 4.9 2.0 - - - -
55A GLY 4.5 7.0 - - - +
157A TRP* 3.5 9.6 - - - +
158A MET* 3.3 42.9 + - + +
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Residues in contact with PRO 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ILE* 1.3 111.7 - - + +
30A ALA* 1.3 58.0 + - - +
52A TRP* 4.3 51.5 - - + +
53A GLY 4.7 12.1 - - - +
75A PHE* 5.8 4.0 - - + -
157A TRP* 3.5 21.2 - - + +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PRO* 1.3 76.4 - - - +
31A ILE* 1.3 79.5 + - + +
156A ALA 3.9 9.2 - - - +
157A TRP* 3.4 6.5 - - - +
158A MET* 3.7 34.3 - - + +
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Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 1.3 93.5 - - + +
32A THR* 1.3 63.6 + - - +
33A TRP* 5.9 1.6 - - + -
139A PHE* 4.6 13.7 - - + -
156A ALA* 2.6 55.0 + - + +
157A TRP* 5.1 0.9 - - - -
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 1.3 76.4 - - - +
33A TRP* 1.3 76.8 + - - +
34A HIS* 3.9 18.6 + - + +
154A TYR 4.5 2.0 - - - -
155A PHE* 2.9 37.1 - - - -
156A ALA 4.7 0.2 - - - +
157A TRP* 5.2 7.6 - - - +
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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