Contacts of the strand formed by residues 117 - 129 (chain A) in PDB entry 5ELI
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 GLU 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.7 3.6 - - - +
114A HIS* 2.9 56.2 + - + +
115A GLY* 3.9 2.4 - - - +
116A SER* 1.3 105.0 + - - +
118A ALA* 1.3 62.8 + - - +
119A ASP* 4.8 1.6 - - - +
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Residues in contact with ALA 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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62A ARG* 4.8 4.9 - - - +
111A GLN* 3.8 28.1 + - + +
112A SER 3.5 5.4 - - - -
113A LEU* 3.8 25.4 - - + -
114A HIS* 5.2 0.2 - - - -
117A GLU* 1.3 77.1 - - - +
119A ASP* 1.3 66.2 + - - +
120A THR* 4.4 1.2 + - - -
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Residues in contact with ASP 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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42A LYS* 6.2 0.2 - - - -
43A HIS* 5.0 12.2 - - + -
46A ARG* 4.7 2.4 + - - -
111A GLN* 3.1 9.8 - - - +
112A SER* 2.9 40.7 + - - +
114A HIS* 2.7 36.7 + - + -
117A GLU* 4.8 1.7 - - - +
118A ALA* 1.3 77.9 + - - +
120A THR* 1.3 64.6 + - - +
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Residues in contact with THR 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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109A GLN* 2.8 30.4 + - + +
110A CYS 3.6 4.0 - - - +
111A GLN* 4.6 2.5 + - - +
118A ALA 5.1 1.2 + - - -
119A ASP* 1.3 74.7 - - - +
121A LEU* 1.3 63.9 + - - +
122A ARG 3.8 22.7 - - - +
123A LYS* 4.8 10.5 - - + +
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Residues in contact with LEU 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 CYS* 4.8 6.5 - - + -
37A PRO 4.5 10.7 - - - +
38A TYR* 3.6 25.6 - - + -
43A HIS* 3.4 37.0 - - + +
48A LYS* 4.2 12.8 - - + -
93A LEU* 4.6 6.3 - - + -
110A CYS* 2.9 18.5 + - + +
111A GLN 3.4 13.9 - - - +
112A SER* 3.3 33.0 - - - +
119A ASP 4.4 0.4 - - - +
120A THR* 1.3 76.1 - - - +
122A ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 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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22A THR* 3.5 35.2 + - + +
24A PHE* 3.3 24.2 - - - -
35A SER* 2.5 39.5 + - - -
36A CYS* 3.6 27.1 - - + +
37A PRO* 4.4 11.9 - - + +
109A GLN* 3.3 9.4 - - - +
110A CYS* 3.2 23.9 + - - +
120A THR* 3.6 6.5 - - - +
121A LEU* 1.3 82.1 - - - +
123A LYS* 1.3 68.2 + - + +
124A VAL* 4.1 12.1 - - + -
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Residues in contact with LYS 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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20A ASN* 3.2 53.5 + - - +
21A THR* 3.6 24.4 - - + +
22A THR* 2.9 29.3 + - - +
107A LEU* 5.8 1.3 - - + -
108A TYR 3.8 6.1 - - - +
109A GLN* 4.4 5.6 - - + +
120A THR* 4.9 9.6 - - + -
122A ARG* 1.3 78.4 - - + +
124A VAL* 1.3 61.8 + - - +
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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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21A THR* 4.6 0.9 - - - -
22A THR* 3.0 23.6 - - - +
24A PHE* 3.6 28.3 - - + -
34A VAL* 5.2 3.4 - - + -
36A CYS* 5.5 3.4 - - - -
50A TRP* 3.8 31.9 - - + -
107A LEU* 3.4 11.7 - - - +
108A TYR* 2.8 49.0 + - + +
109A GLN* 4.7 1.3 - - - +
110A CYS* 5.9 0.7 - - - +
122A ARG* 4.1 15.3 - - + -
123A LYS* 1.3 77.7 - - - +
125A LEU* 1.3 61.3 + - - +
126A VAL* 5.1 2.5 - - + -
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Residues in contact with LEU 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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21A THR* 5.0 9.2 - - - +
22A THR 2.9 8.1 + - - +
23A VAL* 3.6 20.8 - - + -
24A PHE* 2.9 26.9 + - - +
106A GLY* 3.5 9.9 - - - +
107A LEU* 3.7 36.1 - - + -
124A VAL* 1.3 74.8 - - - +
126A VAL* 1.3 68.9 + - - +
127A GLU* 5.2 6.5 - - + +
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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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24A PHE* 3.2 8.7 - - + +
32A LEU* 4.2 15.7 - - + -
34A VAL* 4.9 6.7 - - + -
50A TRP* 5.1 1.6 - - + -
97A LEU* 4.2 24.0 - - + -
100A LEU* 5.4 4.0 - - + -
104A ASP 3.4 10.5 - - - +
105A ALA* 3.5 8.6 - - - +
106A GLY* 2.9 41.9 + - - +
108A TYR* 3.4 22.0 - - + -
124A VAL* 5.1 4.3 - - + -
125A LEU* 1.3 81.6 - - - +
127A GLU* 1.3 65.4 + - - +
128A VAL* 5.7 0.2 - - + -
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Residues in contact with GLU 127 (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 VAL* 3.6 30.1 - - + +
24A PHE 2.9 11.0 + - - +
25A GLN* 3.4 30.0 + - + +
26A GLY* 2.9 23.6 + - - +
100A LEU* 3.7 4.3 - - - +
105A ALA* 4.8 2.0 - - - -
125A LEU* 5.2 7.4 - - + +
126A VAL* 1.3 75.9 - - - +
128A VAL* 1.3 72.8 + - - +
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Residues in contact with VAL 128 (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 GLY 3.0 6.7 - - - +
28A ALA* 4.7 9.9 - - + -
100A LEU* 3.7 17.7 - - + -
101A GLN 3.3 22.9 - - - +
102A PRO* 4.1 19.5 - - + -
105A ALA* 3.8 22.0 - - + +
126A VAL 5.2 0.2 - - - -
127A GLU* 1.3 83.4 - - - +
129A LEU* 1.3 63.8 + - - +
130A ALA 5.4 0.7 - - - +
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Residues in contact with LEU 129 (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 GLY 3.0 10.4 + - - +
27A VAL* 3.6 17.4 - - + +
28A ALA* 2.7 30.6 + - - -
128A VAL* 1.3 75.2 - - - +
130A ALA* 1.3 84.0 + - + +
131A ASP 5.5 1.6 - - - -
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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