Contacts of the strand formed by residues 42 - 50 (chain A) in PDB entry 2YYO
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.1 4.7 - - - +
40A SER* 3.5 5.3 + - - +
41A ASN* 1.3 90.1 - - - +
43A PHE* 1.3 62.3 + - - +
44A GLU* 2.5 45.4 + - + +
108A GLY 3.9 0.2 - - - -
109A CYS 3.4 35.7 - - - -
110A GLY* 4.3 0.4 - - - -
124A PHE* 3.6 29.4 - + + -
126A THR* 2.7 23.6 + - + +
129A GLY* 4.8 2.1 - - - -
161A LEU 3.6 14.6 - - - +
163A ALA* 3.4 33.2 - - + +
164A GLU* 4.1 4.5 - - - -
165A LEU 3.2 28.1 + - - -
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Residues in contact with PHE 43 (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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36A LEU* 4.3 7.9 - - + -
42A TYR* 1.3 77.0 - - - +
44A GLU* 1.3 65.6 + - - +
45A VAL* 3.8 9.9 - - + -
58A VAL* 3.6 30.5 - - + -
59A GLY 3.4 23.6 - - - -
60A LEU* 4.0 8.3 - - + -
108A GLY* 3.3 2.3 - - - -
109A CYS* 2.9 57.3 + - + -
146A PRO* 3.7 32.8 - - + -
147A ALA 4.1 5.4 - - - -
148A VAL* 5.0 0.2 - - + -
159A LEU* 3.9 20.6 - - + -
160A HIS 3.6 12.3 - - - +
161A LEU* 3.9 16.4 - - + +
163A ALA* 4.3 1.8 - - - -
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Residues in contact with GLU 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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42A TYR* 2.5 38.5 + - + +
43A PHE* 1.3 72.9 - - - +
45A VAL* 1.3 64.9 + - - +
46A SER 4.3 0.2 - - - -
106A ARG* 2.9 45.2 + - - +
107A ILE 3.3 6.7 - - - +
108A GLY* 3.9 4.9 - - - -
126A THR* 4.0 3.8 + - - -
129A GLY* 4.2 5.9 + - - -
160A HIS* 2.7 48.6 + - + +
163A ALA* 3.4 23.0 - - + +
164A GLU* 5.0 5.4 - - - +
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Residues in contact with VAL 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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43A PHE* 3.8 12.6 - - + -
44A GLU* 1.3 79.9 - - - +
46A SER* 1.3 64.7 + - - +
47A ILE* 3.9 3.8 + - + +
56A ILE* 5.2 0.7 - - + -
58A VAL* 3.7 41.3 - - + -
106A ARG* 3.2 3.4 - - - -
107A ILE* 2.7 35.5 + - - +
148A VAL* 3.9 10.3 - - + -
157A VAL* 3.4 39.0 - - + -
158A ARG 3.4 5.4 - - - +
159A LEU* 3.9 13.9 - - + -
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Residues in contact with SER 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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45A VAL* 1.3 74.7 - - - +
47A ILE* 1.3 63.7 + - - +
48A VAL* 3.4 3.4 + - - +
104A GLY 6.4 0.4 - - - -
105A ASP 3.9 4.9 - - - -
106A ARG* 3.8 16.3 - - - +
157A VAL* 3.0 7.8 - - - -
158A ARG* 2.9 38.7 + - - -
160A HIS* 3.1 29.4 + - - -
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Residues in contact with ILE 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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45A VAL* 4.9 4.9 - - + +
46A SER* 1.3 70.3 - - - +
48A VAL* 1.3 60.6 + - - +
49A ASP 3.8 19.3 - - - +
50A SER* 3.8 4.5 - - - +
56A ILE* 3.9 23.6 - - + -
82A ALA* 4.1 13.5 - - + -
101A CYS* 3.8 30.1 - - + +
102A ASN 3.6 15.9 - - - +
103A SER* 3.7 18.4 - - - +
104A GLY* 2.9 29.1 + - - -
105A ASP* 2.9 18.3 + - + +
107A ILE* 4.6 9.4 - - + -
156A GLU 3.9 3.1 - - - -
157A VAL* 4.2 4.7 - - + -
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Residues in contact with VAL 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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17A THR* 5.6 0.2 - - + -
46A SER* 3.4 7.2 + - - +
47A ILE* 1.3 75.9 - - - +
49A ASP* 1.3 62.8 + - + +
103A SER* 3.8 11.2 - - - -
104A GLY 4.9 0.5 + - - -
156A GLU* 2.8 40.4 + - + +
157A VAL* 4.1 4.3 - - - -
158A ARG* 3.8 32.8 - - + -
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Residues in contact with ASP 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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47A ILE* 3.5 6.0 - - - +
48A VAL* 1.3 83.5 - - + +
50A SER* 1.3 63.5 + - - +
51A GLY* 2.8 23.2 + - - +
56A ILE* 3.9 1.9 - - - +
103A SER* 3.4 7.7 + - - -
154A GLY* 3.3 22.5 - - - +
155A GLU* 3.3 1.6 - - - -
156A GLU* 2.9 35.2 + - + +
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Residues in contact with SER 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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47A ILE* 3.8 7.8 - - - +
49A ASP* 1.3 73.2 + - - +
51A GLY* 1.3 62.7 + - - +
54A GLY* 2.7 47.1 + - - -
56A ILE* 4.3 4.3 - - - -
101A CYS 5.1 1.6 - - - -
102A ASN* 2.7 36.1 + - - -
103A SER* 3.0 14.9 + - - -
155A GLU* 3.4 9.9 - - - +
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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