Contacts of the strand formed by residues 84 - 92 (chain K) 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 THR 84 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14K VAL* 4.1 1.8 - - - -
16K PHE* 3.3 29.6 - - + -
18K ASP* 4.1 7.0 - - - +
32K THR* 5.6 0.7 - - - -
76K ILE* 3.6 9.7 - - - +
77K ASP* 2.9 33.0 + - - +
80K PHE* 3.4 42.2 + - + -
82K ASP* 2.7 21.0 + - + +
83K SER* 1.3 74.4 + - - +
85K LEU* 1.4 66.3 + - - +
189L GLN* 5.1 3.4 - - - +
193L SER* 5.6 1.6 - - - +
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Residues in contact with LEU 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K VAL* 4.1 22.4 - - + +
8K MET* 3.6 21.1 - - + -
9K LEU* 3.9 20.9 - - + -
14K VAL* 3.6 16.9 - - + +
16K PHE 2.8 9.9 + - - +
17K VAL* 3.0 12.4 - - + +
18K ASP 2.6 31.1 + - - -
74K ALA* 4.1 9.6 - - + -
75K VAL* 3.3 36.8 - - - +
76K ILE* 3.5 11.4 - - + +
84K THR* 1.4 73.2 - - - +
86K ILE* 1.3 61.6 + - - +
87K ILE* 4.4 7.6 - - + -
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Residues in contact with ILE 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ASP* 3.3 11.9 - - + +
20K ARG* 3.5 61.2 - - + +
73K THR 4.0 1.9 - - - +
74K ALA* 3.2 2.6 - - - -
75K VAL* 2.9 46.7 + - + +
77K ASP* 3.5 29.8 - - + +
84K THR* 4.8 0.2 - - - +
85K LEU* 1.3 72.4 - - - +
87K ILE* 1.3 77.6 + - - +
88K ARG* 4.8 7.2 - - - +
202K MET* 3.8 18.8 - - + -
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Residues in contact with ILE 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K VAL* 4.5 14.8 - - + -
17K VAL* 3.8 23.8 - - + -
18K ASP 2.8 11.1 + - - +
19K LEU* 3.4 11.5 - - + -
20K ARG 2.9 23.0 + - - -
38K VAL* 5.8 1.3 - - + -
42K PHE* 4.9 8.3 - - + -
43K PHE* 4.6 11.4 - - + -
69K PRO* 3.9 12.3 - - + -
70K ASP 3.7 20.0 - - - +
71K ALA* 4.9 1.1 - - - +
73K THR* 3.8 8.5 - - - +
74K ALA* 4.1 12.8 - - + -
85K LEU* 4.4 14.1 - - + -
86K ILE* 1.3 83.5 - - - +
88K ARG* 1.3 74.1 + - - +
89K CYS* 3.6 2.6 + - - -
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Residues in contact with ARG 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 3.2 20.6 + - - +
21K PHE* 5.0 1.4 - - - +
22K THR* 4.4 5.7 + - - -
28K GLU* 2.6 46.7 + - - +
70K ASP* 3.1 26.7 + - - +
73K THR* 2.8 30.1 + - + +
86K ILE* 4.8 8.3 - - - +
87K ILE* 1.3 73.2 - - - +
89K CYS* 1.3 65.0 + - - +
105K ARG* 3.8 17.9 - - - +
233K ASP* 3.4 33.1 + - - +
236K GLN* 3.6 15.7 - - - +
237K ILE* 4.0 25.9 - - - +
368K TYR* 3.7 10.7 + - - -
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Residues in contact with CYS 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LEU* 3.6 35.2 - - - -
20K ARG 2.6 13.5 + - - +
21K PHE* 3.8 16.6 - - + +
67K LEU* 3.7 28.3 - - + -
68K MET 3.3 9.2 - - - +
69K PRO* 3.8 22.0 - - - -
87K ILE 3.7 10.1 - - - -
88K ARG* 1.3 76.4 - - - +
90K ASP* 1.3 63.0 + - - +
103K ASP* 5.5 0.3 - - - +
105K ARG* 4.0 15.4 - - - +
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Residues in contact with ASP 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K VAL 3.2 2.9 - - - +
67K LEU* 3.6 1.9 - - - -
68K MET* 2.7 45.2 + - + +
69K PRO 5.2 0.3 - - - +
70K ASP* 4.3 6.2 - - - +
89K CYS* 1.3 73.7 - - - +
91K ILE* 1.3 63.7 + - - +
92K LEU* 3.6 20.0 + - + -
103K ASP* 3.8 8.8 - - - +
105K ARG* 3.1 30.4 + - - +
106K SER* 4.6 3.5 + - - +
109K LYS* 3.1 38.0 + - - +
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Residues in contact with ILE 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K PHE* 4.1 16.4 - - + -
49K PHE* 3.8 17.7 - - + -
57K TRP* 3.8 25.8 - - + -
65K MET* 3.8 30.7 - - + -
66K VAL 3.4 1.8 - - - +
67K LEU* 3.5 31.6 - - + -
90K ASP* 1.3 72.5 - - - +
92K LEU* 1.3 61.2 + - - +
99K GLY* 3.8 2.8 - - - -
100K TYR* 2.9 37.4 + - + +
103K ASP* 2.9 30.9 + - + +
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Residues in contact with LEU 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K MET* 3.3 9.8 - - - +
66K VAL* 3.0 38.2 + - + -
68K MET* 3.5 47.6 - - + -
90K ASP* 4.1 16.2 - - + -
91K ILE* 1.3 78.2 - - - +
93K GLU* 1.3 62.3 + - - +
97K LEU* 3.6 32.1 - - + +
98K GLN 4.3 3.8 - - - +
99K GLY* 3.8 21.5 - - - +
100K TYR* 4.0 3.4 - - - +
106K SER* 4.8 1.3 - - - +
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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