Contacts of the strand formed by residues 124 - 132 (chain A) in PDB entry 4EEJ
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 GLN 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ASN* 2.9 30.8 + - - +
18A GLY* 3.5 28.3 - - - +
19A TRP* 4.1 10.0 - - - -
22A ALA* 3.7 14.6 - - + -
119A LEU 3.9 0.6 - - - +
120A THR* 3.3 5.4 - - - -
121A CYS 2.9 33.9 + - - +
122A GLY 3.3 0.7 - - - +
123A ASP* 1.3 108.3 + - - +
125A VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU 4.1 0.5 - - - +
15A ASN* 3.0 26.9 + - - +
19A TRP* 4.9 0.7 - - - -
118A GLU* 3.9 26.0 - - + +
119A LEU 3.3 9.4 - - - +
120A THR* 4.0 15.9 - - + -
123A ASP 4.1 4.9 + - - +
124A GLN* 1.3 79.7 - - - +
126A CYS* 1.3 69.6 + - - +
127A ARG* 4.1 34.0 + - + +
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Residues in contact with CYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 3.3 26.7 - - - -
14A GLU 3.2 9.4 - - - -
15A ASN 3.7 4.0 - - - +
16A PHE* 3.7 14.6 - - - -
19A TRP* 3.6 27.7 - - + +
117A LEU 3.7 1.0 - - - +
118A GLU* 3.2 5.9 - - - -
119A LEU* 2.8 40.8 + - + +
125A VAL* 1.3 72.4 - - - +
127A ARG* 1.3 61.2 + - - +
128A GLN* 3.6 19.7 - - - -
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Residues in contact with ARG 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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12A SER* 4.1 1.6 + - - +
13A ASN* 3.6 1.7 + - - -
14A GLU* 2.8 72.6 + - + +
117A LEU 3.6 3.4 - - - -
118A GLU* 3.5 33.6 + - + -
125A VAL* 4.1 29.2 + - + +
126A CYS* 1.3 74.0 - - - +
128A GLN* 1.3 61.8 + - - +
129A VAL* 5.4 4.1 - - + +
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Residues in contact with GLN 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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10A MET* 3.5 14.0 - - + +
12A SER 3.4 6.5 - - - +
13A ASN* 3.1 35.4 + - - +
16A PHE* 3.7 15.4 - - - -
38A GLN* 3.8 9.2 + - - +
116A TYR* 3.5 4.7 - - - +
117A LEU* 2.8 51.4 + - + +
119A LEU* 3.9 11.2 - - + +
126A CYS* 3.6 15.5 - - - -
127A ARG* 1.3 73.7 - - - +
129A VAL* 1.4 67.4 + - - +
130A PHE* 3.4 31.6 - - + -
201A RET 5.3 1.8 - - - +
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Residues in contact with VAL 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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10A MET* 3.6 4.3 - - - +
11A GLU* 2.8 38.4 + - + +
12A SER* 3.1 28.3 + - - +
114A LYS* 4.0 28.0 - - + +
115A LEU 3.5 7.0 - - - +
116A TYR* 3.8 31.6 - - + +
127A ARG* 5.4 3.8 - - + +
128A GLN* 1.4 80.8 - - - +
130A PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 130 (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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8A TRP* 3.7 34.5 - - + -
9A GLU 3.2 7.4 - - - +
10A MET* 3.5 42.0 - - + -
11A GLU* 4.3 2.9 - - - +
38A GLN* 4.4 11.4 - - + -
40A LEU* 3.8 26.0 - - + -
53A CYS* 5.8 0.9 - - - -
114A LYS* 3.4 9.3 - - - +
115A LEU* 2.9 50.9 + - + +
117A LEU* 4.1 16.2 - - + -
128A GLN* 3.4 38.6 - - + -
129A VAL* 1.3 78.0 - - - +
131A LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 131 (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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8A TRP* 3.4 3.3 - - - -
9A GLU* 2.9 35.7 + - + +
11A GLU* 3.4 29.7 - - + +
113A ASP* 4.4 6.1 - - + +
114A LYS* 4.8 6.7 - - + -
130A PHE* 1.3 74.4 - - - +
132A LYS* 1.3 68.5 + - - +
133A LYS 3.4 0.3 + - - -
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Residues in contact with LYS 132 (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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3A ASP* 5.2 6.5 + - - -
5A ASN* 3.5 27.5 + - - +
6A GLY* 4.0 9.4 - - - -
7A THR 3.6 11.0 - - - +
8A TRP* 3.5 31.4 - - + -
113A ASP* 3.9 11.0 + - + +
131A LYS* 1.3 77.5 - - - +
133A LYS* 1.3 69.5 + - - +
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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