Contacts of the strand formed by residues 110 - 117 (chain B) in PDB entry 3FN3
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 GLY 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET* 4.9 1.6 - - - -
60B GLU* 3.2 18.4 - - - -
108B ASP 4.0 0.8 + - - -
109B ALA* 1.3 76.6 - - - +
111B VAL* 1.3 64.0 + - - -
112B TYR* 3.8 7.5 - - - -
127B THR* 3.7 4.3 - - - +
128B VAL* 2.8 32.7 + - - +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET* 3.4 1.1 - - - -
60B GLU* 2.8 50.6 + - + +
110B GLY* 1.3 75.8 - - - +
112B TYR* 1.3 64.0 + - - +
113B ARG* 4.1 3.0 + - - +
125B ARG* 3.7 36.3 - - + +
126B ILE 3.6 9.2 - - - +
127B THR* 4.5 16.8 - - + +
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B MET* 4.1 16.0 - - + +
38B ILE* 3.7 25.1 - - + -
57B TRP* 4.6 6.2 - + + -
59B MET* 3.6 25.9 - - + +
64B ILE* 3.6 27.8 - - + -
81B TYR* 4.6 5.1 + + - -
99B LEU* 4.5 5.4 - - + -
101B ILE* 5.1 6.9 - - + +
108B ASP* 2.5 37.6 + - - +
110B GLY 3.8 12.6 - - - -
111B VAL* 1.3 75.1 - - - +
113B ARG* 1.3 60.8 + - - +
124B LYS 3.9 0.2 - - - +
125B ARG* 3.0 8.0 - - - +
126B ILE* 2.7 43.6 + - + +
128B VAL* 3.4 35.7 - - + -
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR 3.7 0.9 - - - +
57B TRP* 3.3 15.4 - - - -
58B GLU* 2.9 65.4 + - - +
59B MET 3.2 14.6 + - - -
60B GLU* 3.6 6.5 - - - +
61B ASP* 2.8 38.0 + - - +
111B VAL* 4.7 2.4 + - + +
112B TYR* 1.3 73.4 - - - +
114B CYS* 1.3 60.1 + - - +
115B MET* 3.2 32.7 - - + +
123B TYR* 5.5 6.1 - - + -
124B LYS 3.6 5.4 - - - +
125B ARG* 3.6 26.7 - - + +
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Residues in contact with CYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 3.8 13.9 - - - -
40B CYS* 2.0 51.6 - - + -
55B VAL* 5.8 0.4 - - + -
56B TYR 3.5 3.4 - - - +
57B TRP* 3.4 26.4 - - + -
113B ARG* 1.3 72.6 - - - +
115B MET* 1.3 61.3 + - - +
116B ILE* 3.8 9.2 - - + -
122B ASP 3.6 1.0 - - - +
123B TYR* 2.9 27.7 - - - +
124B LYS 3.0 12.7 + - - -
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Residues in contact with MET 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 3.8 4.1 - - + +
55B VAL* 3.3 2.3 - - - -
56B TYR* 2.6 62.2 + - + +
58B GLU* 3.4 23.3 - - + +
113B ARG* 3.2 50.9 - - + +
114B CYS* 1.3 76.9 - - - +
116B ILE* 1.3 61.3 + - - +
117B SER 4.3 0.3 + - - -
122B ASP 3.6 4.9 - - - -
123B TYR* 4.5 13.2 - - + -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.8 4.5 - - + -
21B VAL* 3.6 26.9 - - + -
40B CYS* 3.6 32.8 - - + +
42B PHE* 3.9 32.1 - - + -
53B LEU* 4.1 5.6 - - + -
54B ILE 3.3 9.0 - - - +
55B VAL* 3.7 21.5 - - + -
97B ALA* 3.8 13.5 - - + -
114B CYS* 3.8 5.6 - - + -
115B MET* 1.3 77.9 - - - +
117B SER* 1.3 65.1 + - - +
118B TYR 4.2 0.2 - - - -
121B ALA* 3.1 4.1 - - - +
122B ASP 2.8 38.2 + - - +
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA 3.6 2.5 - - - +
53B LEU* 3.6 1.7 - - - -
54B ILE* 2.7 64.5 + - - +
115B MET 4.2 0.4 - - - -
116B ILE* 1.3 73.2 - - - +
118B TYR* 1.3 63.8 + - - +
119B GLY 5.4 0.7 + - - -
120B GLY 3.5 9.1 + - - -
121B ALA* 3.9 13.0 - - - +
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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