Contacts of the strand formed by residues 127 - 131 (chain A) in PDB entry 4EBC
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A HIS* 3.1 22.3 + - + +
33A VAL 3.2 2.0 - - - +
34A ASP* 3.3 19.3 - - - +
122A ARG* 3.4 4.2 - - - +
123A LEU* 3.0 53.0 + - + +
124A GLY 4.3 0.9 - - - +
125A PHE 3.8 0.2 - - - -
126A ASP* 1.3 88.0 + - - +
128A ASN* 1.3 69.7 + - - +
207A LYS* 3.1 22.8 + - - -
501A 0OH 3.9 1.7 + - - -
504A CA 2.7 25.3 - - - -
7P DOC 3.3 25.3 - - - +
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Residues in contact with ASN 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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31A VAL 3.6 0.9 - - - +
32A HIS* 3.4 4.2 - - - -
33A VAL* 2.7 42.4 + - + +
106A SER 5.2 0.6 + - - -
109A VAL* 4.1 21.4 - - - +
110A THR* 3.0 27.0 + - - -
113A LEU* 3.4 27.5 - - + +
120A VAL* 3.5 18.1 - - + +
121A GLU 3.3 3.8 - - - -
122A ARG* 3.7 5.4 - - - +
125A PHE 5.1 3.4 + - - -
126A ASP* 4.2 6.5 + - - +
127A GLU* 1.3 88.3 + - - +
129A PHE* 1.3 62.8 + - - +
130A VAL* 4.9 0.2 - - - -
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Residues in contact with PHE 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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30A ILE* 4.0 6.1 - - + -
31A VAL 3.3 5.4 - - - +
32A HIS* 3.5 42.0 - + + -
120A VAL* 3.4 4.0 - - - +
121A GLU* 2.9 48.7 + - + +
123A LEU* 4.1 25.4 - - + -
128A ASN* 1.3 74.9 - - - +
130A VAL* 1.3 66.0 + - - +
203A LYS* 3.5 60.3 - - + -
207A LYS* 4.1 11.9 - - + -
293A VAL* 3.9 19.2 - - + +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 3.7 0.6 - - - -
31A VAL* 3.0 44.5 + - + +
33A VAL* 5.4 0.2 - - + -
113A LEU* 4.2 19.3 - - + -
117A SER* 3.9 28.7 - - - +
119A VAL 3.9 9.6 - - - +
120A VAL* 3.8 15.0 - - + -
128A ASN 4.9 0.9 - - - +
129A PHE* 1.3 81.0 - - - +
131A ASP* 1.3 61.8 + - - +
132A LEU* 3.2 21.3 + - + -
183A MET* 3.9 19.1 - - + -
293A VAL* 4.5 3.1 - - - -
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Residues in contact with ASP 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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28A ARG* 3.7 16.5 + - - +
30A ILE* 3.3 27.7 - - + +
117A SER* 3.7 19.1 + - - -
119A VAL* 3.9 13.3 + - + +
130A VAL* 1.3 72.7 - - - +
132A LEU* 1.3 58.2 + - - +
133A THR* 2.8 30.8 + - - -
134A GLU* 4.6 2.1 + - - +
135A MET* 5.6 0.5 + - - +
292A PRO* 5.8 0.2 - - - +
293A VAL* 4.0 22.9 + - + +
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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