Contacts of the strand formed by residues 125 - 130 (chain A) in PDB entry 4I5M
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 ASN 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.1 12.5 - - - +
83A ILE* 3.7 23.7 - - + +
84A ILE 3.4 6.7 - - - +
85A PRO* 3.6 18.5 - - - +
86A HIS* 3.6 6.9 + - - -
121A GLU* 3.4 6.9 - - - +
122A ASP* 2.9 29.9 + - - -
123A LYS* 3.7 0.6 + - - +
124A GLU* 1.3 88.7 - - - +
126A ILE* 1.3 61.4 + - - +
127A TYR* 3.1 34.9 + - + -
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Residues in contact with ILE 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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82A LYS 3.3 5.1 - - - +
83A ILE* 3.4 3.5 - - - -
84A ILE* 2.5 59.8 + - + +
85A PRO 5.3 0.4 - - - -
86A HIS* 3.7 19.7 - - + +
89A VAL* 5.4 5.8 - - + -
98A ILE* 4.4 20.6 - - + -
102A ILE* 4.4 2.2 - - + -
119A TYR* 4.4 16.8 - - + -
120A PHE 3.9 2.9 - - - +
121A GLU* 3.3 29.8 - - - +
125A ASN* 1.3 74.0 - - - +
127A TYR* 1.3 63.9 + - - +
128A ILE* 4.1 19.5 - - + -
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Residues in contact with TYR 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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42A ARG* 3.7 8.4 + - - -
44A ILE* 3.6 31.2 - - + +
70A MET* 3.4 27.8 - - + -
82A LYS 3.6 2.0 - - - -
83A ILE* 4.0 18.8 - - + -
119A TYR* 3.0 9.4 - - - +
120A PHE* 2.7 84.8 + + + +
121A GLU* 4.0 0.4 - - - -
122A ASP* 2.6 34.2 + - - -
125A ASN* 3.1 35.4 + - + -
126A ILE* 1.3 76.2 - - - +
128A ILE* 1.3 63.0 + - - +
129A LEU* 4.0 2.0 - - + -
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Residues in contact with ILE 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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80A ALA 4.0 0.2 - - - +
81A ALA* 3.3 5.2 - - - +
82A LYS* 3.0 44.9 + - + -
84A ILE* 3.8 26.9 - - + -
98A ILE* 4.5 3.8 - - + -
101A GLU* 5.0 13.0 - - + +
102A ILE* 3.8 33.9 - - + -
105A HIS* 5.8 0.2 - - - +
116A PHE* 3.6 27.8 - - + -
118A HIS 3.8 2.2 - - - -
119A TYR* 4.4 2.7 - - + -
126A ILE* 4.3 5.2 - - + -
127A TYR* 1.3 76.9 - - - +
129A LEU* 1.3 61.0 + - - +
130A LEU* 3.7 24.6 + - + +
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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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53A TYR* 3.7 27.1 - - + -
70A MET* 4.4 14.4 - - + +
79A TYR* 3.9 29.2 - - + -
80A ALA 4.1 2.2 - - - -
81A ALA* 4.4 11.0 - - + -
116A PHE* 4.2 0.5 - - - -
117A TYR* 3.0 41.9 + - + -
118A HIS* 2.8 34.9 + - + +
120A PHE* 3.7 32.8 - - + -
127A TYR* 4.5 6.5 - - + -
128A ILE* 1.3 74.5 - - - +
130A LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 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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79A TYR* 3.4 9.6 - - - +
80A ALA 2.8 39.5 + - - +
82A LYS* 4.2 16.4 - - + +
101A GLU* 5.4 2.0 - - - +
105A HIS* 3.5 35.7 - - + +
114A VAL* 4.2 1.3 - - + -
115A GLN 3.7 2.9 - - - +
116A PHE* 3.9 15.0 - - + -
117A TYR 5.3 0.2 - - - -
128A ILE* 3.8 28.9 - - + +
129A LEU* 1.3 77.6 - - - +
131A GLU* 1.3 61.1 + - - +
132A TYR 3.3 0.7 + - - -
401A R78 3.6 46.2 - - + +
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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