Contacts of the strand formed by residues 116 - 121 (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 PHE 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLU* 6.5 0.2 - - + -
102A ILE* 3.9 23.8 - - + -
105A HIS* 3.5 48.0 + + + +
106A ARG* 3.7 33.1 - - + +
108A LEU 4.9 0.4 + - - -
109A HIS* 5.3 1.7 - - - -
114A VAL 3.5 5.3 + - - -
115A GLN* 1.3 92.3 + - - +
117A TYR* 1.3 64.6 + - - +
118A HIS* 3.8 9.2 - - - -
119A TYR* 3.5 41.7 - - + -
128A ILE* 3.6 20.9 - - + -
129A LEU 4.9 0.2 - - - -
130A LEU* 3.9 14.4 - - + -
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Residues in contact with TYR 117 (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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51A LYS* 5.4 1.6 + - - -
53A TYR* 4.9 2.7 - + - -
72A ASP* 2.6 31.8 + - + -
74A THR* 5.5 0.7 - - - -
75A ASN* 3.3 11.8 + - - -
79A TYR* 3.3 50.3 - + + -
115A GLN* 3.6 4.8 + - + +
116A PHE* 1.3 79.9 - - - +
118A HIS* 1.3 80.8 + + + +
129A LEU* 3.0 27.7 + - + +
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Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP* 3.5 23.1 + - - -
49A THR* 5.1 8.3 - - + -
51A LYS* 6.2 2.0 - - - -
53A TYR* 3.2 24.2 + + - -
116A PHE* 3.8 9.9 - - - -
117A TYR* 1.3 102.4 - + + +
119A TYR* 1.3 74.3 + - - +
120A PHE* 3.4 21.4 - + + +
128A ILE* 3.8 0.2 - - - -
129A LEU* 2.8 39.7 + - + +
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Residues in contact with TYR 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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99A ASP* 5.2 5.6 + - - -
102A ILE* 3.7 34.3 - - + -
106A ARG* 3.2 31.4 - - - +
116A PHE* 3.5 20.2 - - + -
118A HIS* 1.3 91.0 + - - +
120A PHE* 1.3 72.0 + - - +
121A GLU* 3.2 34.6 + - + +
126A ILE* 4.4 5.4 - - + -
127A TYR 3.0 12.8 - - - +
128A ILE* 4.4 5.6 - - + -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 4.0 15.0 - - + -
45A VAL 4.2 2.2 - - - -
46A ASP* 3.4 44.2 - - + +
47A PRO* 4.3 3.6 - - + -
48A THR* 6.0 1.8 - - + -
53A TYR* 3.5 35.0 - + + -
70A MET* 5.1 1.6 - - - -
118A HIS* 3.4 24.5 - + + +
119A TYR* 1.3 83.1 - - - +
121A GLU* 1.3 66.6 + - - +
122A ASP 5.3 0.2 - - - -
126A ILE* 3.9 0.2 - - - -
127A TYR* 2.7 76.9 + + + +
129A LEU* 3.7 14.1 - - + -
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Residues in contact with GLU 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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46A ASP* 4.8 0.9 - - - +
47A PRO* 3.7 14.9 - - - +
48A THR* 5.1 6.1 - - - +
86A HIS* 3.4 17.1 + - + -
99A ASP* 5.2 4.2 - - - +
119A TYR* 3.2 31.2 + - + +
120A PHE* 1.3 85.5 - - - +
122A ASP* 1.3 62.0 + - - +
125A ASN 3.4 14.8 - - - +
126A ILE* 3.3 28.0 - - + +
127A TYR* 4.0 1.8 - - - -
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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