Contacts of the strand formed by residues 107 - 115 (chain A) in PDB entry 5I7L
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 ASP 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASN* 4.0 13.6 + - - +
106A ILE* 1.3 90.2 - - - +
108A ILE* 1.3 64.1 + - - +
109A LYS 3.9 1.1 - - - +
140A GLN 3.5 3.8 - - - +
141A VAL* 3.6 3.9 - - - +
142A ASN* 2.9 46.8 + - + +
144A PRO* 3.2 29.5 - - - +
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Residues in contact with ILE 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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73A LEU* 4.0 21.7 - - + +
74A LEU* 4.1 30.4 - - + +
106A ILE* 5.8 2.0 - - + -
107A ASP* 1.3 76.9 - - - +
109A LYS* 1.3 63.2 + - - +
110A VAL* 3.6 6.2 + - - +
139A LEU* 3.8 37.9 - - + -
140A GLN 3.7 2.9 - - - +
141A VAL* 3.6 31.2 - - + -
207A LEU* 4.6 16.4 - - + -
91B LEU* 6.3 1.3 - - + -
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Residues in contact with LYS 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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107A ASP* 3.9 2.2 - - - +
108A ILE* 1.3 73.6 - - - +
110A VAL* 1.3 65.0 + - - +
111A THR* 3.8 15.4 + - + -
138A LYS 3.8 0.3 - - - +
139A LEU* 3.7 4.0 - - - -
140A GLN* 3.2 64.1 + - + +
142A ASN* 4.8 5.9 - - - +
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Residues in contact with VAL 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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68A LEU 3.8 16.8 - - - +
69A GLU* 3.6 40.0 + - + +
71A LEU* 4.7 11.0 - - + +
73A LEU* 4.2 13.2 - - + -
108A ILE 3.6 6.9 + - - +
109A LYS* 1.3 78.4 - - - +
111A THR* 1.3 66.1 + - - +
113A PRO 5.9 0.2 - - - -
137A ILE* 3.7 39.0 - - + -
138A LYS 3.5 3.8 - - - +
139A LEU* 3.7 16.4 - - + -
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Residues in contact with THR 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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69A GLU* 5.0 2.0 - - - -
109A LYS* 4.1 25.6 - - + +
110A VAL* 1.3 81.5 - - - +
112A ASP* 1.3 68.0 + - - +
113A PRO* 3.3 6.3 - - - -
137A ILE* 3.8 2.4 - - - -
138A LYS* 2.9 46.5 + - - +
140A GLN* 4.5 17.4 + - + +
152A ARG* 4.3 11.7 + - - +
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Residues in contact with ASP 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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69A GLU* 5.0 0.2 + - - -
111A THR* 1.3 79.5 - - - +
113A PRO* 1.3 74.6 - - - +
114A GLN* 3.3 15.9 + - - +
136A GLY 3.2 10.6 - - - +
137A ILE* 3.8 3.5 - - - -
138A LYS* 3.2 46.2 + - + +
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Residues in contact with PRO 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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65A LEU* 3.9 45.9 - - + +
68A LEU* 4.0 15.9 - - + -
69A GLU* 3.5 37.0 - - + +
110A VAL* 5.9 0.2 - - + -
111A THR 3.3 6.0 - - - +
112A ASP* 1.3 90.6 - - - +
114A GLN* 1.3 64.8 + - - +
136A GLY 3.3 5.2 - - - +
137A ILE* 4.3 4.9 - - + -
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Residues in contact with GLN 114 (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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65A LEU* 4.3 6.2 - - - +
68A LEU* 4.1 4.6 - - - +
112A ASP* 4.1 15.5 - - - +
113A PRO* 1.3 79.5 - - - +
115A LEU* 1.3 65.0 + - - +
116A LEU* 4.0 22.8 - - + +
135A LEU* 3.4 5.4 - - - +
136A GLY* 2.5 47.3 + - - +
156A LYS* 5.8 3.8 - - - -
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Residues in contact with LEU 115 (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 SER* 3.7 29.8 - - - +
59A LEU* 4.5 7.0 - - + -
60A LEU* 3.8 33.9 - - + -
64A LEU* 4.0 19.3 - - + -
65A LEU* 4.2 4.1 - - + +
114A GLN* 1.3 78.9 + - - +
116A LEU* 1.3 81.4 + - - +
118A LEU* 3.8 20.0 - - + -
133A ILE* 3.9 14.4 - - + -
134A PRO 3.7 10.5 - - - +
135A LEU* 4.0 5.2 - - + -
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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