Contacts of the strand formed by residues 114 - 124 (chain A) in PDB entry 1PU5
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 GLY 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A SER* 3.3 3.7 - - - -
43A THR 2.9 32.6 + - - +
112A LYS* 3.4 2.3 + - - -
113A GLU* 1.3 74.8 - - - +
115A THR* 1.3 61.8 + - - -
116A TYR* 3.8 11.5 - - - -
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Residues in contact with THR 115 (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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20A ARG* 4.8 6.8 + - + -
40A VAL* 3.9 22.0 - - + -
41A GLY 3.3 11.0 - - - +
42A SER* 3.6 14.7 - - - -
114A GLY* 1.3 72.5 - - - -
116A TYR* 1.3 70.1 + - - +
117A SER* 4.1 8.2 + - - +
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Residues in contact with TYR 116 (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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39A VAL 3.9 1.4 - - - +
40A VAL* 3.3 4.5 - - - +
41A GLY* 2.8 41.7 + - - +
42A SER* 5.1 1.1 - - - -
43A THR* 4.5 7.4 - - + -
104A GLY 5.8 0.2 - - - -
105A LEU* 4.0 14.6 - - + -
106A PRO* 3.6 38.9 - - + +
111A PHE* 3.8 10.3 - + + -
112A LYS* 2.7 53.6 + - + +
114A GLY* 3.8 19.1 - - - -
115A THR* 1.3 78.2 - - - +
117A SER* 1.3 62.3 + - - +
118A LEU 4.3 0.2 - - - -
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Residues in contact with SER 117 (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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39A VAL 3.7 2.7 - - - -
40A VAL* 3.8 23.5 - - - +
103A TYR* 4.2 6.1 - - - +
105A LEU* 3.6 20.8 - - - +
115A THR* 4.1 8.0 + - - +
116A TYR* 1.3 76.4 + - - +
118A LEU* 1.3 60.3 + - - +
119A PRO* 3.7 8.7 - - - +
73B TYR* 4.5 7.0 + - - -
88B MET* 4.1 16.9 + - - -
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Residues in contact with LEU 118 (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 LEU* 4.0 31.6 - - + +
38A SER* 3.2 3.5 - - - -
39A VAL* 2.8 48.4 + - + +
99A PRO* 3.7 17.3 - - + -
100A LEU* 5.2 6.1 - - + -
103A TYR* 3.8 16.2 - - + -
105A LEU* 3.7 20.0 - - + -
117A SER* 1.3 73.4 - - - +
119A PRO* 1.3 70.3 - - - +
121A SER* 3.5 19.5 - - - +
123A PHE* 4.4 13.9 - - + -
88B MET* 3.6 4.5 - - - +
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Residues in contact with PRO 119 (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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103A TYR* 3.5 43.2 - - + +
117A SER* 3.7 5.6 - - - +
118A LEU* 1.3 90.5 - - - +
120A LYS* 1.3 70.0 + - - +
121A SER* 3.0 15.1 + - - -
73B TYR* 3.9 9.2 - - - +
81B HIS 5.1 0.7 - - - +
84B ASP* 3.3 12.8 - - + +
85B VAL* 3.7 33.9 - - + +
88B MET* 3.6 16.8 - - + -
89B LEU* 6.5 0.2 - - + -
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Residues in contact with LYS 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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23A THR* 3.9 18.7 - - - +
25A GLU* 2.9 36.8 + - - +
36A THR* 3.8 11.2 - - + -
37A LEU 3.3 7.2 - - - -
38A SER* 3.4 12.1 - - - -
103A TYR* 4.8 4.0 + - - -
119A PRO* 1.3 72.5 - - - +
121A SER* 1.3 59.9 + - - +
80B GLU* 4.2 3.1 - - - +
81B HIS* 3.2 49.8 + - + +
84B ASP* 2.8 38.0 + - + +
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Residues in contact with SER 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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36A THR* 3.3 5.1 - - - -
37A LEU 2.7 33.3 + - - +
99A PRO* 3.7 21.4 - - - +
103A TYR* 3.9 6.9 - - - -
118A LEU* 3.5 13.7 - - - +
119A PRO 3.0 14.3 + - - -
120A LYS* 1.3 72.9 + - - +
122A GLU* 1.3 60.4 + - - +
123A PHE* 3.4 25.4 - - - -
80B GLU* 3.4 9.8 + - - -
81B HIS* 4.7 0.4 - - - -
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASN* 3.1 41.3 + - + -
35A VAL 3.4 6.5 - - - +
36A THR* 4.0 14.8 + - - +
99A PRO* 5.8 1.2 - - - +
121A SER* 1.3 75.2 - - - +
123A PHE* 1.3 68.5 + - - +
80B GLU* 2.8 26.7 + - - +
81B HIS* 4.7 10.4 + - - +
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Residues in contact with PHE 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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34A ASN* 3.4 4.5 - - - -
35A VAL* 2.8 46.2 + - + +
37A LEU* 3.8 32.5 - - + -
98A GLU 5.0 1.3 - - - -
99A PRO* 3.7 37.2 - - + -
100A LEU* 6.5 0.4 - - + -
118A LEU* 4.4 4.9 - - + -
121A SER* 3.4 29.8 - - - -
122A GLU* 1.3 76.6 - - - +
124A VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 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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33A GLY 4.0 4.9 - - - +
34A ASN* 2.8 24.7 - - - +
35A VAL* 5.3 0.2 - - - -
123A PHE* 1.3 76.0 - - - +
125A VAL* 1.3 77.0 + - - +
126A PRO* 3.5 6.9 - - - +
127A ASP* 4.4 8.7 - - - +
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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