Contacts of the strand formed by residues 56 - 62 (chain A) in PDB entry 1UMK
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ILE* 2.9 27.5 + - + -
53A SER* 3.2 18.1 + - - -
55A ASP* 1.3 89.4 + - - +
57A ARG* 1.3 77.1 + - - +
108A VAL* 3.6 17.0 - - + -
109A ILE 3.1 14.8 - - - +
110A LYS* 3.7 16.4 - - - +
216A LEU* 3.4 34.2 - - + +
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Residues in contact with ARG 57 (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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49A ARG* 3.6 10.2 - - + +
50A GLU 3.2 8.3 - - - +
51A ILE* 3.9 28.3 - - + +
52A ILE* 3.6 8.8 - - - +
53A SER 3.1 26.7 + - - -
54A HIS 3.5 13.1 + - - -
55A ASP 4.3 3.1 - - - -
56A THR* 1.3 84.1 + - - +
58A ARG* 1.3 61.5 + - - +
59A PHE* 3.6 30.6 + - + -
107A LEU 3.7 0.2 - - - +
108A VAL* 3.3 4.0 - - - -
109A ILE* 2.9 31.4 + - - +
111A VAL* 3.8 17.5 - - - +
113A PHE* 3.7 14.2 - - - -
131A GLU* 2.7 40.5 + - - +
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Residues in contact with ARG 58 (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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48A ASP* 3.2 25.3 + - - +
49A ARG* 3.5 4.5 - - - -
50A GLU* 2.6 79.6 + - + +
52A ILE* 3.7 14.4 - - + +
57A ARG* 1.3 73.2 - - - +
59A PHE* 1.3 64.0 + - - +
60A ARG* 3.4 30.6 - - - +
96A ILE* 4.2 16.2 - - + -
106A ASP* 3.1 39.8 + - - +
107A LEU 3.3 9.6 - - - +
108A VAL* 4.4 1.8 - - + +
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Residues in contact with PHE 59 (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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46A LEU* 3.9 20.9 - - + -
48A ASP 3.5 1.6 - - - -
49A ARG* 3.4 47.8 - - + -
57A ARG* 3.6 20.4 - - + -
58A ARG* 1.3 78.3 - - - +
60A ARG* 1.3 59.7 + - - +
61A PHE* 3.6 22.4 - + + -
105A VAL 3.8 1.2 - - - +
106A ASP* 3.6 3.1 - - - -
107A LEU* 2.8 36.4 + - + +
109A ILE* 3.6 41.3 - - + -
111A VAL* 5.2 1.1 - - + -
130A LEU* 4.0 34.5 - - + -
131A GLU* 4.1 5.8 - - - -
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Residues in contact with ARG 60 (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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46A LEU* 3.5 4.9 - - - +
47A ILE* 2.8 49.8 + - + -
48A ASP* 3.0 23.7 + - + -
58A ARG* 3.4 22.0 - - - +
59A PHE* 1.3 74.1 - - - +
61A PHE* 1.3 59.3 + - - +
104A PHE* 3.4 54.7 - - + -
105A VAL 3.4 4.3 - - - +
106A ASP* 2.9 37.7 + - - +
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Residues in contact with PHE 61 (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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44A LEU* 3.8 22.4 - - + -
45A ARG 3.1 5.4 - - - +
46A LEU* 3.8 33.2 - - + -
47A ILE* 4.2 3.1 - - - -
59A PHE* 3.6 32.8 - - + -
60A ARG* 1.3 75.9 - - - +
62A ALA* 1.3 63.1 + - - +
104A PHE* 3.3 4.7 - - - +
105A VAL* 2.9 48.7 + - + +
107A LEU* 3.9 20.2 - - + -
130A LEU* 3.9 24.7 - - + -
133A MET* 4.1 6.1 - - + -
139A ILE* 3.6 23.8 - - + -
141A PHE* 3.8 14.6 - + + -
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Residues in contact with ALA 62 (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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44A LEU* 3.6 23.2 - - - +
45A ARG* 2.8 18.8 + - + +
47A ILE* 3.8 29.8 - - + +
61A PHE* 1.3 73.5 - - - +
63A LEU* 1.3 70.1 + - - +
103A GLY 3.7 8.1 - - - +
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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