Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 2UYK
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 LEU 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.9 0.5 - - - -
34A PRO* 3.2 28.5 - - + +
46A VAL* 5.3 1.1 - - + +
49A GLN* 3.7 29.4 - - + +
50A ALA* 3.9 18.4 - - + +
53A SER* 3.4 22.0 - - - +
54A LEU* 6.4 0.2 - - + -
76A VAL* 4.5 4.0 - - + -
77A PHE 3.1 12.8 - - - +
78A ILE* 3.9 9.9 - - + -
87A ILE* 4.2 26.9 - - + -
113A LEU* 3.5 5.6 - - - -
117A VAL* 3.4 7.6 - - - +
118A LYS* 1.3 82.5 - - + +
120A GLU* 1.3 62.1 + - - +
121A ILE* 3.8 25.4 - - + -
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Residues in contact with GLU 120 (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 GLY* 3.6 19.9 - - - -
32A GLN 3.3 5.4 - - - -
33A ILE* 3.9 9.3 - - + +
75A THR 3.6 2.3 - - - +
76A VAL* 3.7 1.0 - - - -
77A PHE* 2.9 38.2 + - + +
113A LEU* 3.5 21.2 - - + +
114A PRO* 3.6 6.8 - - - +
119A LEU* 1.3 74.7 - - - +
121A ILE* 1.3 63.1 + - - +
122A GLU 4.2 0.2 - - - -
106C SER* 3.4 15.9 - - - -
107C CYS 2.7 33.7 + - - +
108C VAL* 4.1 6.7 - - - -
1129C SER* 2.9 27.1 + - - -
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Residues in contact with ILE 121 (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 SER 3.8 0.7 - - - +
31A GLY* 4.0 0.9 - - - -
32A GLN* 2.7 40.7 + - - +
53A SER* 4.0 11.2 - - - -
54A LEU* 3.7 31.4 - - + +
57A VAL* 3.7 16.7 - - + +
74A MET* 3.8 33.0 - - + -
75A THR 3.3 7.2 - - - +
76A VAL* 4.2 22.0 - - + -
87A ILE* 5.9 0.7 - - + -
91A TYR* 5.0 4.0 - - + -
119A LEU* 3.8 28.5 - - + -
120A GLU* 1.3 77.5 - - - +
122A GLU* 1.3 61.0 + - - +
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Residues in contact with GLU 122 (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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29A THR* 3.8 13.9 - - - +
30A SER 4.0 0.7 - - - -
31A GLY* 4.1 4.2 - - - -
73A LYS* 5.4 2.1 - - - -
74A MET* 3.3 5.4 - - - +
75A THR* 2.9 61.7 + - - +
77A PHE* 4.4 11.6 - - + -
120A GLU 4.2 0.6 - - - -
121A ILE* 1.3 74.8 - - - +
123A ALA* 1.3 61.4 + - - +
124A ILE* 5.9 4.5 - - + +
73C LYS* 2.9 24.8 + - - -
75C THR* 4.2 2.9 + - - -
106C SER* 2.7 35.4 + - - +
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Residues in contact with ALA 123 (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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27A VAL 4.0 0.2 - - - +
28A PHE* 3.7 0.9 - - - -
29A THR* 3.0 41.7 + - + +
57A VAL* 3.6 21.5 - - + -
61A VAL* 4.9 1.6 - - + -
71A ILE* 4.2 11.2 - - + -
73A LYS 3.3 5.4 - - - +
74A MET* 3.4 24.5 - - + -
121A ILE 4.3 0.2 + - - -
122A GLU* 1.3 74.3 - - - +
124A ILE* 1.3 68.8 + - - +
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Residues in contact with ILE 124 (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 MET* 4.1 25.8 - - + -
27A VAL 3.3 9.9 - - - +
28A PHE* 3.6 30.5 - - + -
71A ILE* 3.5 3.8 - - - -
72A ILE* 2.8 47.2 + - + +
73A LYS* 2.9 33.7 + - + +
122A GLU* 5.9 4.9 - - - +
123A ALA* 1.3 79.6 - - - +
125A ALA* 1.3 60.1 + - - +
28B PHE* 3.9 25.4 - - + -
124B ILE* 6.0 0.2 - - + -
124C ILE* 5.9 1.1 - - + -
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Residues in contact with ALA 125 (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 MET* 3.3 4.7 - - - +
27A VAL* 2.7 39.8 + - + +
61A VAL* 4.5 11.7 - - + -
66A LEU* 3.9 20.6 - - + -
70A ASP* 3.2 22.4 - - + +
71A ILE* 3.9 10.5 - - + -
72A ILE 4.2 0.2 - - - +
124A ILE* 1.3 75.9 - - - +
126A VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 126 (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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25A SER 3.3 12.1 - - - +
26A MET* 4.1 11.9 - - + -
66A LEU* 4.2 4.2 - - - +
70A ASP* 2.9 29.9 + - - +
72A ILE* 3.6 29.4 - - + -
125A ALA* 1.3 78.3 - - - +
127A ARG* 1.3 62.9 + - - +
128A SER* 3.6 8.1 + - - +
2B LYS* 3.8 17.9 - - + -
23B LEU* 3.5 36.6 - - + -
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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