Contacts of the strand formed by residues 109 - 116 (chain A) in PDB entry 1F89
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 ILE 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.2 1.8 - - + -
65A ARG* 3.7 55.4 - - - +
68A SER* 3.7 17.9 - - - +
100A PRO* 6.3 0.2 - - + -
101A GLU 2.8 12.3 - - - +
102A LEU* 3.4 26.9 - - + -
107A ASP 4.0 0.2 + - - -
108A LYS* 1.3 73.4 - - - +
110A TYR* 1.3 61.4 + - - +
147A THR* 3.1 35.7 - - + +
148A LEU* 3.3 12.8 - - + +
149A SER* 3.2 23.0 + - - -
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Residues in contact with TYR 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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64A PHE* 4.8 0.3 - - - -
100A PRO* 3.6 4.0 - - - +
101A GLU* 2.7 41.0 + - + +
103A ASP* 4.6 7.9 - - + -
106A THR* 4.7 2.2 + - - +
108A LYS* 3.4 48.1 + - + +
109A ILE* 1.3 77.4 - - - +
111A ASN* 1.3 60.6 + - - +
112A THR* 3.8 9.6 - - - +
127A ARG* 3.0 55.4 - - + +
128A LYS 5.4 0.2 - - - -
148A LEU* 4.6 8.5 - - - +
149A SER* 3.2 30.1 - - - +
150A PRO 3.0 28.0 + - - -
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Residues in contact with ASN 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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53A GLU* 3.7 9.5 + - - +
54A CYS* 4.3 5.1 - - - +
59A TYR* 5.1 1.2 - - - -
64A PHE* 3.5 26.6 - - + -
98A THR* 2.8 42.7 + - - +
99A ILE 4.1 4.1 + - - -
110A TYR* 1.3 74.4 - - - +
112A THR* 1.3 59.2 + - - +
128A LYS* 3.0 38.6 + - + +
131A LEU* 6.6 0.2 - - + -
148A LEU* 4.1 18.2 - - + +
149A SER 5.0 1.8 + - - -
168A ILE* 3.5 18.0 - - - +
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Residues in contact with THR 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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72A ASN* 5.6 0.2 - - - -
98A THR* 2.8 22.3 - - - -
99A ILE* 2.9 23.1 + - - +
101A GLU* 2.6 28.1 + - - +
110A TYR* 3.8 4.2 - - - +
111A ASN* 1.3 76.9 - - - +
113A SER* 1.3 64.6 + - - +
114A ILE* 3.8 7.9 + - + +
125A LYS* 3.7 27.8 - - + -
126A HIS 3.1 28.7 - - - +
127A ARG* 3.3 16.1 - - + +
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Residues in contact with SER 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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95A VAL* 3.5 26.5 - - - +
97A GLY* 3.7 2.3 + - - -
98A THR* 3.3 18.8 + - - +
112A THR* 1.3 71.2 - - - +
114A ILE* 1.3 61.8 + - - +
115A ILE* 3.2 11.1 - - - +
125A LYS* 3.2 1.9 - - - -
126A HIS* 2.9 28.8 + - - -
166A VAL* 3.9 17.6 - - - +
168A ILE* 3.7 18.0 - - - +
192A PRO* 4.0 3.1 - - - +
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Residues in contact with ILE 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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72A ASN* 3.1 32.1 - - - +
79A SER 4.6 0.2 - - - +
80A VAL* 4.5 8.3 - - - -
83A LEU* 3.5 17.0 - - + -
95A VAL 3.6 0.7 - - - -
96A GLY* 2.6 43.9 + - - +
98A THR 4.4 1.8 - - - +
99A ILE* 4.0 28.0 - - + -
112A THR* 3.8 9.8 + - + +
113A SER* 1.3 75.0 + - - +
115A ILE* 1.3 58.7 + - - +
116A PHE* 3.4 31.3 - - + -
122A LEU* 3.8 9.0 - - + -
124A ASP 4.2 3.1 - - - -
125A LYS* 4.4 9.0 - - + -
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Residues in contact with ILE 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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93A ILE* 4.4 2.7 - - + -
94A LEU 3.6 5.4 - - - +
95A VAL* 4.2 18.6 - - + -
113A SER* 3.2 31.9 - - - +
114A ILE* 1.3 75.1 - - - +
116A PHE* 1.3 75.3 + - - +
122A LEU* 3.2 7.6 - - - +
123A ILE* 2.9 25.7 + - + -
124A ASP 3.1 17.9 + - - +
125A LYS* 4.2 4.7 - - - -
126A HIS 4.7 1.1 - - - +
157A ILE* 4.1 42.4 - - + -
164A PHE* 4.3 11.7 - - + -
166A VAL* 4.3 15.0 - - + -
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Residues in contact with PHE 116 (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 VAL* 3.5 35.0 - - + -
83A LEU* 3.7 20.4 - - + -
84A SER* 3.8 17.9 - - - -
87A ALA* 3.7 21.3 - - + -
93A ILE* 3.2 25.6 - - - +
94A LEU* 2.9 27.2 + - + +
96A GLY 4.6 0.4 - - - -
114A ILE* 3.4 45.8 - - + -
115A ILE* 1.3 76.9 - - - +
117A ASN* 1.3 60.7 + - - +
120A GLY 3.8 11.2 - - - -
121A LYS 3.3 7.0 - - - +
122A LEU* 3.8 24.2 - - + -
123A ILE* 3.8 4.5 - - - +
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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