Contacts of the strand formed by residues 49 - 56 (chain A) in PDB entry 3WUZ
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 VAL 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.0 17.0 - - + -
42A SER 5.2 2.0 - - - +
43A ALA* 4.0 7.6 - - + -
48A SER* 1.3 78.1 - - - +
50A GLU* 1.3 75.4 + - - +
51A ILE* 4.4 10.3 - - + -
110A LEU 3.6 1.0 - - - +
111A ARG* 3.3 3.9 - - - +
112A ILE* 3.0 40.6 + - + +
115A LEU* 3.9 18.2 - - + -
147A LEU* 4.0 34.3 - - + -
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Residues in contact with GLU 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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41A LEU* 3.3 19.2 - - - +
48A SER* 6.1 0.4 - - - +
49A VAL* 1.3 77.7 - - - +
51A ILE* 1.3 61.1 + - - +
52A PRO* 3.4 6.8 - - + +
109A PHE* 3.4 52.3 - - + -
110A LEU 3.4 4.9 - - - -
111A ARG* 4.2 16.2 + - + +
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Residues in contact with ILE 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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37A GLN* 3.9 3.4 - - - +
41A LEU* 4.3 7.2 - - + -
49A VAL* 4.4 13.9 - - + -
50A GLU* 1.3 74.7 - - - +
52A PRO* 1.3 67.8 - - + +
71A TRP* 3.6 28.9 - - + -
109A PHE* 3.2 3.0 - - - -
110A LEU* 2.8 39.0 + - + +
112A ILE* 4.0 18.6 - - + -
123A TYR* 3.8 35.2 - - + -
145A THR* 3.5 33.7 - - + +
147A LEU* 5.0 4.7 - - + -
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Residues in contact with PRO 52 (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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37A GLN* 3.5 10.0 - - - +
38A PRO* 3.3 48.2 - - + +
41A LEU* 4.2 4.3 - - + -
50A GLU* 3.4 12.8 - - + +
51A ILE* 1.3 86.4 - - - +
53A PHE* 1.3 61.0 + - - +
108A GLY 3.3 10.8 - - - +
109A PHE* 3.7 7.9 - - + -
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Residues in contact with PHE 53 (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 VAL* 4.1 10.3 - - + -
36A THR 3.2 10.1 - - - +
37A GLN* 4.0 10.8 - - + -
52A PRO* 1.3 76.1 - - - +
54A SER* 1.3 68.5 + - - +
55A PHE* 4.7 4.9 - - + -
69A ILE* 3.9 23.3 - - + -
71A TRP* 3.7 19.3 - + + -
99A LEU* 4.1 15.7 - - + -
101A TRP* 3.7 30.3 - + - -
106A LYS 5.0 1.6 - - - -
107A SER* 3.3 11.0 - - - -
108A GLY* 2.9 58.1 + - - +
109A PHE* 3.7 5.6 - - - -
125A CYS* 4.0 15.5 - - + -
127A VAL* 5.0 5.2 - - + -
201A IPA 5.5 1.1 - - - -
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Residues in contact with SER 54 (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 GLY 3.6 1.2 - - - +
35A VAL* 3.3 4.0 - - - +
36A THR* 2.8 47.6 + - - -
53A PHE* 1.3 78.9 - - - +
55A PHE* 1.3 64.7 + - - +
56A TYR* 5.7 1.4 - - - +
106A LYS 3.5 8.2 + - - -
107A SER* 4.3 5.9 - - - +
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Residues in contact with PHE 55 (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 GLY* 3.4 17.7 - - - -
35A VAL* 4.1 7.9 - - + +
53A PHE* 5.1 5.2 - - + -
54A SER* 1.3 77.7 + - - +
56A TYR* 1.3 60.4 + - - +
57A TYR* 3.6 33.5 + + + -
61A LEU* 5.1 3.4 - - + -
106A LYS* 2.7 41.4 + - + +
127A VAL* 3.9 17.9 - - + -
129A LEU* 4.0 19.7 - - + -
139A TRP* 3.5 48.0 - + - -
201A IPA 3.8 30.7 - - + +
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Residues in contact with TYR 56 (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 MET* 3.7 38.6 - - + -
32A LEU 3.9 7.9 - - - +
33A TYR* 3.3 35.9 - + - +
34A GLY* 2.9 40.4 + - - +
36A THR* 6.1 1.3 - - - +
54A SER* 4.2 2.2 - - - +
55A PHE* 1.3 74.9 - - - +
57A TYR* 1.3 64.0 + - - +
58A PRO* 3.7 32.8 - - + +
106A LYS* 6.2 0.4 - - + -
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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