Contacts of the strand formed by residues 16 - 22 (chain B) in PDB entry 1FPY
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 PHE 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A SER* 3.6 42.6 - - - -
196A CYS* 4.0 18.8 - - + -
197A LEU* 3.7 25.8 - - + -
209A HIS* 4.6 5.4 - + - -
14B VAL* 2.9 9.3 - - - +
15B LYS* 1.3 95.7 - - + +
17B VAL* 1.3 62.0 - - - +
32B THR* 3.6 24.7 - - + -
33B ILE 3.4 2.9 - - - -
34B PRO* 3.9 24.2 - - + -
35B ALA 3.9 0.9 - - - +
82B ASP* 4.0 13.9 - - + -
83B SER 3.3 3.0 + - - -
84B THR* 3.3 14.5 - - + -
85B LEU 2.8 29.4 + - - -
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Residues in contact with VAL 17 (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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5B VAL* 6.4 0.4 - - + -
9B LEU* 4.3 18.4 - - + -
16B PHE* 1.3 81.2 - - - +
18B ASP* 1.3 62.4 + - - +
19B LEU* 3.6 24.5 + - + +
31B VAL 3.5 1.6 - - - +
32B THR* 3.3 4.5 - - - +
33B ILE* 2.6 49.7 + - + +
35B ALA* 4.3 10.8 - - - -
38B VAL* 3.9 25.1 - - + -
42B PHE* 5.2 0.2 - - + -
85B LEU* 3.0 13.9 - - + +
87B ILE* 3.8 20.6 - - + -
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Residues in contact with ASP 18 (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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17B VAL* 1.3 71.2 - - - +
19B LEU* 1.3 66.2 + - - +
20B ARG* 2.8 33.8 + - - +
30B HIS* 2.9 30.0 - - - +
31B VAL 3.3 4.0 - - - +
32B THR* 2.7 30.8 + - + +
80B PHE* 4.0 9.8 - - + -
84B THR* 4.1 12.7 + - - +
85B LEU 2.6 13.5 + - - +
86B ILE* 3.3 8.6 - - + +
87B ILE 2.8 27.9 + - - -
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Residues in contact with LEU 19 (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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17B VAL* 3.6 28.0 - - + +
18B ASP* 1.3 72.9 - - - +
20B ARG* 1.3 59.7 + - - +
21B PHE* 4.8 2.5 - - - -
30B HIS* 2.9 5.5 - - - -
31B VAL* 2.7 63.0 + - + +
33B ILE* 4.6 20.2 - - + -
42B PHE* 4.1 27.8 - - + -
47B LYS* 5.1 6.5 - - + -
67B LEU* 4.3 15.3 - - + -
87B ILE* 3.4 10.1 - - + +
89B CYS* 3.6 23.1 - - - -
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Residues in contact with ARG 20 (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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182A VAL* 4.2 5.4 - - - +
183A PRO* 5.8 0.4 - - - +
18B ASP* 2.8 22.8 + - - +
19B LEU* 1.3 81.7 - - - +
21B PHE* 1.3 59.8 + - - +
28B GLU* 3.4 31.4 + - + +
29B GLN 3.0 7.2 - - - +
30B HIS* 3.6 13.0 - - + +
77B ASP* 2.6 27.3 + - - -
80B PHE* 3.6 8.7 - - - -
86B ILE* 3.5 40.1 - - + +
87B ILE 2.9 8.9 + - - +
88B ARG* 3.2 14.5 - - - +
89B CYS* 2.6 33.6 + - - -
202B MET* 5.2 0.6 - - - +
240B TYR* 3.4 39.2 + - - -
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Residues in contact with PHE 21 (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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180A PHE* 4.0 17.9 - + - -
19B LEU 4.8 2.5 - - - -
20B ARG* 1.3 79.2 - - - +
22B THR* 1.3 66.0 + - - +
23B ASP* 4.6 0.4 - - - -
28B GLU* 3.5 3.7 - - - +
29B GLN* 2.6 70.0 + - + +
30B HIS* 4.7 1.3 - - - -
31B VAL* 5.5 1.1 - - + -
49B PHE* 4.3 9.0 - + - -
54B ILE* 3.7 21.1 - - + -
57B TRP* 3.6 34.3 - + - -
67B LEU* 3.6 26.7 - - + -
88B ARG* 5.0 4.9 - - - +
89B CYS 3.8 17.0 - - - +
91B ILE* 4.1 14.4 - - + -
103B ASP* 6.1 0.7 - - - +
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Residues in contact with THR 22 (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 PHE* 1.3 84.9 + - - +
23B ASP* 1.3 75.2 + - - +
26B GLY* 3.4 15.3 - - - +
27B LYS 3.8 2.5 - - - +
28B GLU* 4.3 0.2 - - - +
57B TRP* 3.6 7.8 - - - -
88B ARG* 4.4 5.9 + - - -
103B ASP* 4.5 3.8 + - - +
104B PRO* 3.5 18.7 - - + +
105B ARG* 5.9 4.1 - - - +
236B GLN* 3.1 34.4 + - - +
366B ASN* 4.4 2.0 - - - +
368B TYR* 3.4 35.8 + - + -
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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