Contacts of the strand formed by residues 28 - 34 (chain H) 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 GLU 28 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20H ARG* 3.4 23.0 + - + -
21H PHE 3.5 8.5 - - - +
22H THR* 4.3 0.4 - - - +
26H GLY 3.4 4.0 + - - -
27H LYS* 1.3 71.6 - - - +
29H GLN* 1.3 74.0 + - - +
88H ARG* 2.6 36.7 + - - +
236H GLN* 3.6 39.9 - - - +
237H ILE* 5.1 1.9 + - - +
240H TYR* 4.1 11.3 + - - +
181I PRO* 4.0 0.3 - - - +
182I VAL* 3.2 47.9 + - + +
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Residues in contact with GLN 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ARG* 3.0 8.8 - - - +
21H PHE* 2.6 71.2 + - + +
23H ASP* 4.1 14.8 + - + +
27H LYS* 2.6 44.0 + - - +
28H GLU* 1.3 89.2 + - - +
30H HIS* 1.3 62.3 + - - +
54H ILE* 5.0 7.3 - - + +
179I TYR 3.0 24.8 - - - +
180I PHE* 3.0 16.9 - - + +
181I PRO* 3.4 7.1 - - - +
182I VAL* 4.2 1.3 - - - -
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Residues in contact with HIS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H ASP* 2.9 42.0 - - - +
19H LEU 2.9 9.6 - - - +
20H ARG* 3.6 10.8 - - + -
21H PHE* 5.2 1.1 - - - -
29H GLN* 1.3 78.1 - - - +
31H VAL* 1.3 66.3 + - - +
32H THR* 3.9 1.3 - - - -
80H PHE* 5.1 0.2 - + - -
180I PHE* 3.1 31.7 + - - +
181I PRO 3.4 16.7 + - - -
182I VAL* 3.7 9.1 - - + -
183I PRO* 3.5 17.7 - - + -
186I ASP* 3.0 26.1 + - - -
189I GLN* 3.2 27.4 + - + +
192I ARG* 3.7 3.9 + - - -
210I HIS* 4.9 2.2 - - - +
211I HIS* 5.8 2.1 + - + -
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Residues in contact with VAL 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H VAL 3.5 1.2 - - - +
18H ASP* 3.3 1.7 - - - +
19H LEU* 2.7 68.8 + - + +
21H PHE* 5.5 1.8 - - + -
30H HIS* 1.3 80.3 - - - +
32H THR* 1.3 70.8 + - - +
33H ILE* 3.9 8.7 + - + -
67H LEU* 4.0 17.0 - - + -
180I PHE* 4.2 18.2 - - + -
208I ALA* 5.1 2.2 - - + -
209I HIS 3.8 12.1 - - - +
210I HIS* 4.0 16.4 - - + +
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Residues in contact with THR 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H PHE* 3.6 28.9 - - + -
17H VAL 3.3 12.8 - - - +
18H ASP* 2.7 12.6 + - + +
30H HIS* 3.9 0.9 - - - -
31H VAL* 1.3 72.3 - - - +
33H ILE* 1.3 73.8 + - - +
84H THR* 5.6 1.6 - - - -
189I GLN* 2.6 32.1 + - - +
208I ALA* 3.2 1.4 - - - +
209I HIS* 2.9 62.4 + - - +
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Residues in contact with ILE 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H PHE* 3.4 5.0 - - - +
17H VAL* 2.6 45.8 + - + +
19H LEU* 4.6 21.3 - - + -
31H VAL* 4.5 11.2 - - + -
32H THR* 1.3 79.9 - - - +
34H PRO* 1.3 73.4 - - - +
37H GLN* 3.6 15.9 - - + +
38H VAL* 4.0 18.4 - - + -
42H PHE* 5.5 3.6 - - + -
47H LYS* 5.0 16.2 - - + +
207I GLU 3.4 12.1 - - - +
208I ALA* 3.1 26.7 - - + -
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Residues in contact with PRO 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LYS 3.7 8.3 - - - +
16H PHE* 3.9 15.7 - - + -
32H THR 4.4 0.2 - - - +
33H ILE* 1.3 95.2 - - - +
35H ALA* 1.3 67.2 + - - +
36H HIS* 3.5 26.0 - - + +
37H GLN* 2.9 17.9 + - + +
200I GLU* 4.7 3.1 - - - +
206I VAL* 3.0 36.8 - - + +
207I GLU 3.1 22.0 - - - +
208I ALA* 3.9 2.7 - - - +
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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