Contacts of the strand formed by residues 121 - 131 (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 ALA 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.5 5.2 + - - +
116B ILE 3.1 11.7 - - - +
117B SER* 3.9 16.6 - - - +
120B GLY* 1.3 76.5 - - - +
122B ASP* 1.3 64.4 + - - +
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Residues in contact with ASP 122 (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* 3.1 12.9 - - + +
20B THR* 3.5 17.1 - - - +
21B VAL* 3.2 35.2 + - + +
114B CYS 3.6 0.5 - - - +
115B MET* 3.6 1.2 - - - -
116B ILE 2.8 37.6 + - - +
121B ALA* 1.3 75.1 - - - +
123B TYR* 1.3 89.1 + - - +
124B LYS* 3.0 24.1 + - - -
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Residues in contact with TYR 123 (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* 4.5 0.7 - - - -
113B ARG* 5.5 6.7 - - + -
114B CYS 2.9 17.3 - - - +
115B MET* 4.5 13.9 - - + -
122B ASP* 1.3 90.9 + - - +
124B LYS* 1.3 87.9 + - - +
125B ARG* 3.9 38.0 + - + -
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Residues in contact with LYS 124 (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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20B THR* 5.0 4.2 - - - +
21B VAL* 3.0 42.4 + - + +
22B THR* 4.6 4.7 - - - +
23B VAL* 4.0 21.5 - - + +
40B CYS* 4.6 2.5 - - - -
112B TYR 3.9 0.3 - - - +
113B ARG* 3.6 2.6 - - - -
114B CYS* 3.0 30.6 + - - -
122B ASP* 3.0 27.3 + - - -
123B TYR* 1.3 85.3 + - - +
125B ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 125 (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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23B VAL* 4.9 4.0 - - - +
26B ASP* 4.1 13.0 - - - +
111B VAL* 3.7 25.0 - - + +
112B TYR 3.0 10.8 - - - +
113B ARG* 3.6 25.5 - - + +
123B TYR* 3.9 31.2 + - + -
124B LYS* 1.3 77.9 - - - +
126B ILE* 1.3 65.0 + - - +
127B THR* 5.5 0.2 + - - -
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Residues in contact with ILE 126 (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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23B VAL* 3.6 18.2 - - + -
25B LYS 3.2 20.0 - - - +
26B ASP 3.6 2.7 - - - +
28B TYR* 3.4 29.8 - - + -
38B ILE* 4.2 14.4 - - + -
39B GLU 3.4 38.8 - - - +
40B CYS* 4.5 1.6 - - - -
57B TRP* 4.3 13.0 - - + -
111B VAL* 3.6 2.9 - - - -
112B TYR* 2.7 43.4 + - + +
125B ARG* 1.3 73.8 - - - +
127B THR* 1.3 69.9 + - - +
128B VAL* 3.8 9.7 + - + -
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Residues in contact with THR 127 (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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26B ASP 2.7 19.5 + - - -
27B LEU* 3.4 18.5 - - + +
28B TYR 2.8 26.2 + - - +
110B GLY* 3.7 9.0 - - - +
111B VAL* 4.5 17.4 - - + +
125B ARG 4.2 1.0 + - - -
126B ILE* 1.3 71.9 - - - +
128B VAL* 1.3 70.1 + - - +
129B LYS* 4.6 13.0 - - + -
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Residues in contact with VAL 128 (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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28B TYR* 3.4 16.2 - - + +
30B VAL* 5.3 3.1 - - + -
36B MET* 3.4 42.4 - - + -
38B ILE* 4.0 0.9 - - + -
108B ASP 3.9 12.6 - - - +
109B ALA* 3.2 10.4 - - - +
110B GLY 2.8 30.4 + - - +
112B TYR* 3.4 23.6 - - + -
126B ILE* 3.9 14.4 - - + -
127B THR* 1.3 81.7 - - - +
129B LYS* 1.3 62.8 + - - +
130B VAL* 4.5 10.5 - - + -
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Residues in contact with LYS 129 (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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27B LEU* 3.8 29.5 - - + +
28B TYR 2.7 12.8 + - - +
29B VAL* 3.4 20.0 - - + +
30B VAL* 3.0 27.7 + - - +
109B ALA* 4.7 1.1 - - - -
127B THR* 4.1 13.3 - - + -
128B VAL* 1.3 73.0 - - - +
130B VAL* 1.3 62.5 + - - +
131B ASN* 3.9 6.1 + - - +
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Residues in contact with VAL 130 (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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30B VAL* 3.4 12.3 - - + +
32B TYR* 3.9 18.4 - - + +
104B VAL* 3.8 22.9 - - + -
105B LYS 3.4 30.5 - - - +
106B LEU* 3.9 24.4 - - + +
108B ASP 4.2 2.9 - - - +
109B ALA* 3.8 29.3 - - + +
128B VAL* 3.9 7.1 + - + -
129B LYS* 1.3 74.6 - - - +
131B ASN* 1.3 63.1 + - - +
132B ALA 4.0 0.3 + - - -
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Residues in contact with ASN 131 (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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29B VAL* 4.2 21.8 - - + +
30B VAL 3.1 9.5 + - - +
31B GLU* 3.5 10.2 - - - +
32B TYR* 2.9 23.5 + - - -
129B LYS* 3.9 5.3 + - - +
130B VAL* 1.3 76.3 + - - +
132B ALA* 1.3 59.5 + - - +
133B PRO* 3.3 10.4 - - + +
213B ARG* 4.1 23.4 - - - +
216B PRO* 5.2 14.9 - - - +
218B GLU* 4.6 8.6 + - - +
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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