Contacts of the strand formed by residues 106 - 112 (chain F) in PDB entry 5IJ7
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 ARG 106 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B CYS* 3.3 34.2 - - - +
84B SER 4.6 4.2 + - - -
85B VAL* 5.7 1.6 - - - +
98B LEU* 4.0 18.0 - - - +
76F GLU* 4.7 6.3 - - - +
77F ASP* 2.8 38.0 + - - +
78F HIS* 4.0 33.8 - - + +
101F THR 4.4 0.4 - - - -
102F VAL* 3.6 4.3 - - - -
103F GLY 2.9 33.5 + - - +
104F SER* 3.2 1.5 + - - -
105F ASN* 1.3 85.7 - - - +
107F VAL* 1.3 68.0 + - - +
108F THR* 4.4 13.1 + - - +
123F SER* 3.6 12.7 + - - -
124F TYR 3.2 14.1 - - - +
125F VAL* 4.0 11.2 - - + -
133F PHE* 3.6 4.4 - - - -
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Residues in contact with VAL 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.7 4.0 - - + -
100F ALA* 5.1 0.4 - - + -
101F THR 3.4 8.3 - - - +
102F VAL* 4.1 2.7 - - + -
106F ARG* 1.3 78.9 - - - +
108F THR* 1.3 63.8 + - - +
109F LEU* 4.2 8.5 - - + -
123F SER* 3.3 3.1 + - - -
124F TYR* 2.8 46.4 + - + -
133F PHE* 3.9 14.4 - - + -
149F LEU* 3.6 30.7 - - + -
151F VAL* 3.6 35.2 - - + -
161F ILE* 4.2 12.8 - - + -
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Residues in contact with THR 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 5.1 1.3 - - + -
76F GLU* 3.3 29.1 + - - +
99F PHE 4.0 0.3 - - - +
100F ALA* 3.3 3.1 - - - -
101F THR* 2.7 39.0 + - - +
106F ARG* 4.4 8.3 + - - +
107F VAL* 1.3 78.4 + - - +
109F LEU* 1.3 65.2 + - - +
110F TYR* 3.5 25.1 - - + +
120F LEU* 3.5 20.4 - - + -
122F GLN 3.4 10.3 - - - +
123F SER* 3.3 14.8 + - - +
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 3.7 14.8 - - + -
98F VAL* 5.0 3.1 - - + -
99F PHE 3.5 3.4 - - - +
100F ALA* 4.4 0.4 - - + -
107F VAL* 4.2 9.0 - - + -
108F THR* 1.3 80.3 - - - +
110F TYR* 1.3 68.3 + - - +
120F LEU* 4.0 0.5 - - - -
121F LEU* 3.0 26.8 + - + -
122F GLN* 2.8 32.9 + - + +
124F TYR* 4.4 15.5 - - + -
138F TRP* 3.8 24.9 - - + -
149F LEU* 4.1 23.1 - - + -
161F ILE* 6.3 0.7 - - + -
163F PRO* 3.7 29.8 - - + -
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Residues in contact with TYR 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 3.3 22.1 - - + +
74F LEU* 3.6 17.7 - - + -
76F GLU* 2.5 30.0 + - - -
98F VAL* 3.1 13.1 - - - +
99F PHE* 2.9 70.1 + + + -
101F THR* 4.0 6.5 - - - -
108F THR* 3.5 21.3 - - + +
109F LEU* 1.3 77.6 - - - +
111F GLU* 1.3 58.7 + - - +
112F CYS 4.4 0.2 - - - -
118F ILE* 3.7 17.0 - - + -
119F ARG 3.4 3.8 - - - -
120F LEU* 3.9 28.0 - - + -
121F LEU* 4.3 4.0 - - - +
420F ILE* 3.4 19.1 - - + +
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Residues in contact with GLU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 5.7 0.7 - - - +
68B VAL 3.5 20.6 - - - +
69B HIS* 5.2 2.9 + - - -
96F PRO* 3.2 40.5 - - + +
97F LEU 3.7 2.2 - - - -
98F VAL* 3.9 11.0 - - + +
110F TYR* 1.3 74.1 - - - +
112F CYS* 1.3 63.5 + - - +
113F HIS* 3.1 25.7 + - + -
117F GLU 3.9 0.3 - - - +
118F ILE* 3.5 3.8 - - - -
119F ARG* 2.8 59.0 + - + +
121F LEU* 3.8 21.3 - - + +
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Residues in contact with CYS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F PHE* 4.0 9.4 - - - -
96F PRO* 4.2 11.8 - - - +
97F LEU* 2.8 27.7 + - + +
99F PHE* 3.6 32.8 - - - -
111F GLU* 1.3 71.8 - - - +
113F HIS* 1.3 70.8 + - - +
117F GLU 3.8 3.4 - - - -
118F ILE* 4.8 2.0 - - - +
410F ILE* 3.7 34.8 - - + -
422F ARG* 4.0 14.6 - - - -
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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