Contacts of the strand formed by residues 105 - 113 (chain A) in PDB entry 1I04
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A THR* 5.7 1.6 - - + -
99A SER* 3.8 23.6 - - - -
100A VAL 4.1 4.7 - - - -
101A THR* 4.8 10.3 - - - +
104A GLY* 1.3 71.7 - - - -
106A ASN* 1.3 63.3 + - - +
107A THR* 3.5 29.2 - - + -
124A ILE 3.6 1.6 - - - +
125A ASN* 3.5 1.7 - - - -
126A GLU* 2.7 65.2 + - + +
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Residues in contact with ASN 106 (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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56A PHE* 3.6 11.5 - - - -
99A SER* 2.9 9.6 - - - -
100A VAL* 2.9 60.6 + - + +
102A TYR* 2.8 39.4 + - - +
104A GLY 3.7 1.0 + - - -
105A PHE* 1.3 75.6 - - - +
107A THR* 1.3 65.4 + - - +
108A PHE* 5.5 0.2 - - + -
123A LEU* 3.8 19.5 - - + +
124A ILE 3.4 3.6 - - - +
125A ASN* 2.8 30.8 + - - +
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Residues in contact with THR 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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92A THR* 4.9 2.0 - - + -
94A LYS* 6.2 1.3 - - - +
97A GLU* 3.7 25.8 + - - +
98A TYR 3.0 9.2 - - - -
99A SER* 4.3 4.3 - - - -
105A PHE* 3.5 31.4 - - + -
106A ASN* 1.3 81.0 - - - +
108A PHE* 1.3 62.9 + - - +
123A LEU* 3.4 1.1 - - - +
124A ILE* 2.9 49.6 + - - +
126A GLU* 5.4 2.2 - - - +
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Residues in contact with PHE 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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70A LEU* 4.5 11.2 - - + -
72A LEU* 4.1 21.5 - - + -
89A ALA* 3.6 33.7 - - + -
96A GLY 3.8 0.3 - - - +
97A GLU* 3.3 4.9 - - - +
98A TYR* 2.7 60.8 + + + +
100A VAL* 4.6 14.1 - - + -
107A THR* 1.3 78.1 - - - +
109A THR* 1.3 74.6 + - - +
110A ILE* 4.9 8.5 - - + -
121A ALA* 4.9 10.5 - - + -
122A HIS 3.1 16.8 - - - +
123A LEU* 3.7 22.9 - - + -
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Residues in contact with THR 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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23A SER* 3.7 3.4 - - - -
24A THR* 3.8 21.5 - - + -
96A GLY 3.5 18.4 - - - +
97A GLU* 3.9 20.4 - - + +
108A PHE* 1.3 81.7 - - - +
110A ILE* 1.3 68.6 + - - +
111A PRO* 3.6 10.7 - - - +
121A ALA* 3.5 6.2 - - - +
122A HIS* 3.0 39.2 + - - +
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Residues in contact with ILE 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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22A SER* 3.2 0.5 - - - -
23A SER* 2.7 46.4 + - - -
24A THR* 6.1 0.2 - - - -
28A PHE* 3.8 14.8 - - + -
33A ILE* 3.6 30.3 - - + -
63A ILE* 6.1 0.4 - - + -
70A LEU* 5.2 7.9 - - + -
96A GLY 5.5 0.2 - - - +
98A TYR* 5.5 4.0 - - + -
108A PHE* 4.9 10.8 - - + -
109A THR* 1.3 78.3 - - - +
111A PRO* 1.3 62.6 - - - +
112A LYS 3.2 1.9 + - - +
113A THR* 4.0 21.5 - - + -
119A LEU* 3.8 30.3 - - + -
120A MET 3.4 14.8 - - - +
121A ALA* 4.9 2.0 - - + -
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Residues in contact with PRO 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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22A SER* 3.0 23.6 - - - -
24A THR* 5.6 2.2 - - + +
109A THR* 3.5 16.6 - - - +
110A ILE* 1.3 87.0 - - - +
112A LYS* 1.3 70.8 + - - +
120A MET* 3.1 16.8 - - + +
122A HIS* 3.8 20.6 - - + +
135A MET* 4.6 1.1 - - + -
155A LEU* 4.0 28.9 - - + -
159A HIS* 5.8 4.3 - - + -
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Residues in contact with LYS 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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20A GLU* 3.4 16.9 + - + +
21A ALA* 3.4 18.0 - - - +
22A SER* 4.9 1.8 - - - +
110A ILE* 3.1 2.7 - - - -
111A PRO* 1.3 91.3 + - + +
113A THR* 1.3 62.2 + - - +
118A PHE* 3.6 19.1 - - + -
120A MET* 2.7 48.5 + - - +
151A ARG* 2.9 31.2 - - - +
155A LEU* 5.5 2.5 - - + -
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Residues in contact with THR 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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20A GLU* 3.2 3.1 - - - -
21A ALA 3.0 35.9 + - - +
28A PHE* 4.0 18.6 - - + -
33A ILE* 4.5 3.1 - - + -
37A TRP* 4.3 0.7 - - - -
110A ILE* 4.0 11.9 - - + -
112A LYS* 1.3 76.5 - - - +
114A ASP* 1.3 60.7 + - - +
115A TYR* 3.0 28.1 + - + -
118A PHE* 2.7 29.4 + - - -
119A LEU* 3.7 22.1 - - - +
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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