Contacts of the strand formed by residues 43 - 51 (chain A) in PDB entry 2UUY
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 HIS 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 2.7 27.2 + - - +
38A LEU 3.5 5.4 - - - -
39A ASN* 3.6 7.0 - - - +
42A TYR* 1.3 74.2 - - - +
44A PHE* 1.3 58.8 + - - +
45A CYS 3.1 28.9 + - - -
46A GLY* 4.1 1.6 - - - -
75A ILE* 3.8 23.9 - - + +
141A TRP* 3.8 40.9 - + + +
151A TYR* 6.0 0.4 - + - -
195A GLY* 2.9 29.4 + - - -
41B ARG* 2.8 44.9 + - - +
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Residues in contact with PHE 44 (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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38A LEU* 3.0 47.6 + - + -
39A ASN 3.7 11.7 - - - -
40A SER* 3.8 24.0 - - - -
42A TYR* 3.7 13.2 - + + -
43A HIS* 1.3 78.0 - - - +
45A CYS* 1.3 83.5 + - + +
61A CYS* 3.2 24.0 - - + -
63A LYS* 3.8 15.5 - - + -
66A ILE* 3.8 20.6 - - + -
195A GLY* 4.3 1.4 - - - -
40B ALA* 3.7 0.7 - - - -
41B ARG* 2.9 45.7 + - - +
42B PHE* 3.8 17.7 - + + -
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Residues in contact with CYS 45 (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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38A LEU* 2.8 28.9 + - + -
43A HIS* 3.1 14.8 + - - -
44A PHE* 1.3 101.7 - - + +
46A GLY* 1.3 64.4 + - - +
61A CYS* 2.0 52.9 - - + -
195A GLY 4.1 5.8 - - - -
197A SER* 3.3 7.6 - - - +
40B ALA* 3.7 17.5 - - - -
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Residues in contact with GLY 46 (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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35A GLN* 4.0 9.4 - - - -
36A VAL 3.3 13.2 - - - -
38A LEU* 3.6 8.2 - - - +
43A HIS* 4.5 3.6 - - - -
45A CYS* 1.3 75.9 - - - +
47A GLY* 1.3 52.8 + - - -
57A SER* 2.8 27.2 + - - -
195A GLY 4.1 5.2 + - - -
196A ASP* 4.4 2.0 + - - -
197A SER 2.7 12.9 + - - +
198A GLY* 3.4 10.2 - - - -
199A GLY* 4.1 3.6 - - - -
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Residues in contact with GLY 47 (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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34A TYR 3.7 0.9 - - - +
35A GLN* 3.7 8.2 + - - +
36A VAL* 2.9 42.0 + - - +
38A LEU* 5.1 0.7 - - - -
46A GLY* 1.3 73.9 - - - -
48A SER* 1.3 63.2 + - - -
55A VAL* 4.0 4.5 - - - -
56A VAL 3.2 7.9 - - - -
57A SER* 4.3 0.4 - - - -
198A GLY 3.2 13.7 + - - -
199A GLY* 3.9 2.5 - - - -
200A PRO* 4.0 1.0 - - - +
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Residues in contact with SER 48 (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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34A TYR* 3.3 6.7 - - - -
36A VAL* 4.9 0.2 - - - -
47A GLY* 1.3 74.3 - - - -
49A LEU* 1.3 63.7 + - - +
50A ILE* 3.4 2.6 + - - +
55A VAL* 3.3 4.8 - - - +
56A VAL* 2.8 40.2 + - - -
123A ILE* 4.1 9.2 - - - -
198A GLY 4.6 0.5 + - - -
199A GLY 4.1 1.4 - - - -
200A PRO* 3.2 32.6 - - - +
207A LEU* 3.5 29.7 - - - +
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Residues in contact with LEU 49 (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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33A PRO 4.9 1.3 - - - +
34A TYR* 2.8 18.0 + - - +
36A VAL* 4.4 7.7 - - + +
47A GLY 4.3 0.2 - - - -
48A SER* 1.3 69.9 - - - +
50A ILE* 1.3 57.8 + - - +
51A ASN 3.1 24.7 - - - +
54A TRP 3.6 9.0 - - - +
55A VAL* 3.9 17.0 - - + -
70A LEU* 4.3 10.5 - - + -
110A LEU* 4.2 16.4 - - + -
114A ALA* 4.6 1.3 - - + -
116A LEU* 3.7 28.9 - - + -
120A VAL* 3.8 19.1 - - + -
121A ALA 3.8 18.6 - - - +
122A SER* 3.2 1.8 - - - +
123A ILE* 2.9 28.2 + - - +
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Residues in contact with ILE 50 (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 SER 3.4 4.0 + - - +
49A LEU* 1.3 77.7 - - - +
51A ASN* 1.3 65.9 + - - +
54A TRP* 3.0 26.0 + - + +
55A VAL 4.6 0.2 - - - +
56A VAL* 3.8 30.3 - - + -
107A LEU* 4.0 5.2 - - + -
122A SER* 3.5 12.3 + - - -
123A ILE* 4.0 19.1 - - + +
125A LEU* 4.0 24.8 - - + +
207A LEU* 4.1 11.0 - - + -
236A ILE* 3.8 28.9 - - + -
240A ILE* 3.8 15.9 - - + -
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Residues in contact with ASN 51 (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 LEU* 3.1 24.1 - - - +
50A ILE* 1.3 79.0 + - - +
52A SER* 1.3 63.7 + - - +
53A GLN* 2.9 18.0 + - - +
54A TRP* 3.0 26.9 + - - +
116A LEU* 4.8 2.5 - - - -
122A SER* 4.0 9.9 - - - -
240A ILE* 3.6 31.7 - - - +
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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