Contacts of the strand formed by residues 16 - 22 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 2.9 9.4 - - - +
15A LYS* 1.3 102.3 - - + +
17A VAL* 1.3 61.0 + - - +
32A THR* 3.6 24.7 - - + -
33A ILE 3.4 2.7 - - - -
34A PRO* 3.9 24.0 - - + -
35A ALA 3.9 1.1 - - - +
82A ASP* 4.0 15.3 - - + -
83A SER 3.3 3.0 + - - -
84A THR* 3.3 14.8 - - + -
85A LEU 2.8 28.4 + - - -
193F SER* 3.6 44.2 - - - -
196F CYS* 4.1 17.9 - - + -
197F LEU* 3.7 20.6 - - + -
209F HIS* 4.6 4.7 - + - -
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Residues in contact with VAL 17 (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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5A VAL* 6.4 0.2 - - + -
9A LEU* 4.3 18.6 - - + -
16A PHE* 1.3 81.1 - - - +
18A ASP* 1.3 62.7 + - - +
19A LEU* 3.6 24.4 + - + +
31A VAL 3.5 1.7 - - - +
32A THR* 3.3 4.4 - - - +
33A ILE* 2.6 49.4 + - + +
35A ALA* 4.3 10.1 - - - -
38A VAL* 3.9 24.7 - - + -
42A PHE* 5.2 0.4 - - + -
85A LEU* 3.0 14.8 - - + +
87A ILE* 3.8 19.7 - - + -
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Residues in contact with ASP 18 (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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16A PHE 4.2 0.6 - - - -
17A VAL* 1.3 72.1 - - - +
19A LEU* 1.3 66.2 + - - +
20A ARG* 2.8 31.9 + - - +
30A HIS* 2.9 29.9 - - - +
31A VAL 3.3 3.8 - - - +
32A THR* 2.7 30.0 + - + +
80A PHE* 4.0 9.7 - - + -
84A THR* 4.1 12.3 + - - +
85A LEU 2.6 13.1 + - - +
86A ILE* 3.3 9.6 - - + +
87A ILE 2.8 28.4 + - - +
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Residues in contact with LEU 19 (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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17A VAL* 3.6 27.1 - - + +
18A ASP* 1.3 72.7 - - - +
20A ARG* 1.3 60.3 + - - +
21A PHE* 4.8 2.6 - - - -
30A HIS* 2.9 5.4 - - - -
31A VAL* 2.7 62.5 + - + +
33A ILE* 4.6 20.6 - - + -
42A PHE* 4.1 27.8 - - + -
47A LYS* 5.1 6.5 - - + -
67A LEU* 4.3 15.5 - - + -
87A ILE* 3.4 9.9 - - + +
89A CYS* 3.6 24.2 - - - -
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Residues in contact with ARG 20 (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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18A ASP* 2.8 22.0 + - - +
19A LEU* 1.3 81.0 - - - +
21A PHE* 1.3 60.1 + - - +
28A GLU* 3.4 28.3 + - - +
29A GLN 3.0 7.2 - - - +
30A HIS* 3.6 13.7 - - + +
77A ASP* 2.6 27.1 + - - -
80A PHE* 3.6 8.5 - - - -
86A ILE* 3.5 40.3 - - + +
87A ILE 2.9 9.3 + - - +
88A ARG* 3.2 15.2 - - - +
89A CYS* 2.6 34.3 + - - -
202A MET* 5.2 1.2 - - - +
240A TYR* 3.4 39.6 + - - -
182F VAL* 4.0 7.6 - - - -
183F PRO* 6.0 0.2 - - - -
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Residues in contact with PHE 21 (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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19A LEU 4.8 2.5 - - - -
20A ARG* 1.3 80.0 - - - +
22A THR* 1.3 65.9 + - - +
23A ASP* 4.6 0.4 - - - -
28A GLU* 3.5 3.7 - - - +
29A GLN* 2.6 70.2 + - + +
30A HIS* 5.2 1.8 - - - -
31A VAL* 5.5 0.4 - - + -
49A PHE* 4.3 8.7 - + - -
54A ILE* 3.7 20.2 - - + -
57A TRP* 3.6 34.5 - + - -
67A LEU* 3.6 27.1 - - + -
88A ARG* 5.0 4.0 - - - +
89A CYS 3.8 16.4 - - - +
91A ILE* 4.1 14.8 - - + -
103A ASP* 6.1 0.4 - - - +
180F PHE* 3.9 18.8 - + - -
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Residues in contact with THR 22 (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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21A PHE* 1.3 85.8 + - - +
23A ASP* 1.3 75.7 + - - +
26A GLY* 3.4 14.8 - - - +
27A LYS 3.8 2.9 - - - +
28A GLU* 4.3 0.4 - - - +
57A TRP* 3.6 8.0 - - - -
88A ARG* 4.4 5.7 + - - -
103A ASP* 4.5 4.2 + - - +
104A PRO* 3.5 18.3 - - + +
105A ARG* 5.9 3.8 - - - +
236A GLN* 3.1 33.6 + - - +
366A ASN* 4.4 2.2 - - - +
368A TYR* 3.4 36.6 + - + -
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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