Contacts of the strand formed by residues 106 - 114 (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 GLY 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.9 8.3 - - - -
105A ALA* 1.3 78.4 - - - +
107A LEU* 1.3 60.1 + - - -
108A TYR* 3.6 7.6 - - - -
125A LEU* 3.5 9.1 - - - +
126A VAL* 2.9 35.8 + - - +
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Residues in contact with LEU 107 (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 18.2 - - + +
52A ARG* 3.7 5.3 - - - +
53A GLN* 2.9 57.2 + - + +
55A GLY 4.4 8.7 - - - +
56A GLU* 5.0 9.6 - - - +
106A GLY* 1.3 71.4 - - - -
108A TYR* 1.3 65.6 + - - +
123A LYS* 5.8 1.3 - - + -
124A VAL 3.4 18.2 - - - +
125A LEU* 3.7 24.0 - - + -
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Residues in contact with TYR 108 (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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50A TRP* 3.3 51.6 - + + -
51A CYS 3.4 8.1 - - - +
52A ARG* 3.1 51.3 + - + +
53A GLN* 4.7 1.3 - - - +
60A CYS* 5.7 0.4 - - - -
63A VAL* 5.0 4.0 - - + -
97A LEU* 5.3 8.9 - - + +
104A ASP* 2.5 24.4 + - - +
106A GLY* 3.6 16.2 - - - -
107A LEU* 1.3 80.2 - - - +
109A GLN* 1.3 65.3 + - - +
123A LYS* 3.8 1.6 - - - +
124A VAL* 2.8 34.2 + - + +
126A VAL* 3.4 32.1 - - + -
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Residues in contact with GLN 109 (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 ALA 4.1 0.2 - - - +
50A TRP* 3.7 6.5 - - - -
51A CYS* 2.9 52.1 + - - +
53A GLN* 3.6 21.0 + - - +
60A CYS* 3.7 6.3 - - - +
108A TYR* 1.3 76.4 - - - +
110A CYS* 1.3 62.1 + - - +
111A GLN* 3.2 23.8 + - + +
120A THR* 2.8 31.3 + - + +
122A ARG 3.3 16.4 - - - +
123A LYS* 4.4 5.3 - - + +
124A VAL* 4.8 2.2 - - - +
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Residues in contact with CYS 110 (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* 2.1 52.3 - - + -
49A ALA 3.6 4.9 - - - -
50A TRP* 3.8 24.5 - - - -
93A LEU* 4.0 17.9 - - + -
95A ILE* 4.5 4.7 - - - -
109A GLN* 1.3 73.9 - - - +
111A GLN* 1.3 64.6 + - - +
120A THR* 3.6 3.8 - - - +
121A LEU* 2.9 31.9 + - + -
122A ARG* 3.2 8.2 + - - +
124A VAL* 6.1 0.2 - - - -
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Residues in contact with GLN 111 (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 LYS* 3.2 8.5 - - - +
49A ALA* 2.9 38.9 + - + +
51A CYS* 3.7 23.9 - - - +
60A CYS* 4.6 6.3 - - - +
62A ARG* 4.2 13.7 + - - -
93A LEU* 5.0 0.2 - - - +
109A GLN* 3.2 28.7 + - + +
110A CYS* 1.3 81.3 - - - +
112A SER* 1.3 59.2 + - - +
113A LEU* 3.9 12.4 - - + +
118A ALA* 3.8 23.3 + - + +
119A ASP 3.1 11.9 - - - +
120A THR* 4.6 2.0 + - - -
121A LEU* 3.4 5.8 - - - +
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Residues in contact with SER 112 (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 HIS* 3.0 37.6 + - - +
46A ARG* 3.0 23.6 - - - +
47A ARG 3.6 4.0 - - - -
48A LYS* 4.0 4.7 - - - +
111A GLN* 1.3 72.1 - - - +
113A LEU* 1.3 61.1 + - - +
114A HIS* 3.9 3.7 + - - -
118A ALA* 3.5 0.9 - - - -
119A ASP* 2.9 35.3 + - - +
121A LEU* 3.3 19.1 - - - +
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Residues in contact with LEU 113 (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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46A ARG* 3.4 21.7 - - - +
47A ARG* 2.9 51.1 + - + +
48A LYS 4.5 1.1 - - - +
49A ALA* 3.8 25.6 - - + -
62A ARG* 3.3 32.1 - - - +
65A SER* 4.8 2.2 - - - -
111A GLN* 3.9 8.1 - - + +
112A SER* 1.3 75.2 - - - +
114A HIS* 1.3 59.8 + - - +
115A GLY 4.4 3.4 - - - +
117A GLU 3.7 6.3 - - - +
118A ALA* 3.8 22.4 - - + -
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Residues in contact with HIS 114 (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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46A ARG* 3.0 45.1 + - + +
112A SER 4.1 5.4 - - - -
113A LEU* 1.3 74.1 - - - +
115A GLY* 1.3 67.0 + - - +
116A SER 3.4 0.2 + - - -
117A GLU* 2.9 39.4 + - + +
119A ASP* 2.7 41.6 + - - -
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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