Contacts of the strand formed by residues 28 - 34 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C PRO* 3.9 0.5 - - - +
182C VAL* 3.2 48.0 + - + +
20D ARG* 3.4 23.3 + - + -
21D PHE 3.5 8.7 - - - +
22D THR* 4.3 0.4 - - - +
26D GLY 3.4 3.6 + - - -
27D LYS* 1.3 72.9 - - - +
29D GLN* 1.3 73.5 + - - +
88D ARG* 2.6 37.5 + - - +
236D GLN* 3.5 38.2 - - - +
237D ILE* 5.1 1.9 + - - +
240D TYR* 4.1 10.9 - - - +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C TYR 3.0 24.6 - - - +
180C PHE* 3.0 17.1 - - + +
181C PRO* 3.3 7.6 - - - +
182C VAL* 4.2 0.9 - - - -
20D ARG* 3.0 8.7 - - - +
21D PHE* 2.6 73.4 + - + +
23D ASP* 4.1 14.7 + - + +
27D LYS* 2.6 43.9 + - - +
28D GLU* 1.3 88.0 + - - +
30D HIS* 1.3 62.7 + - - +
54D ILE* 5.0 6.8 - - + +
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Residues in contact with HIS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 3.0 31.6 + - - +
181C PRO 3.3 17.4 + - - -
182C VAL* 3.6 9.1 - - + -
183C PRO* 3.3 19.5 - - + +
186C ASP* 3.0 25.2 + - - -
189C GLN* 3.3 27.1 + - + +
192C ARG* 3.7 3.7 + - - -
210C HIS* 4.9 2.1 - - - +
211C HIS 5.8 1.7 + - - -
18D ASP* 2.9 42.4 - - - +
19D LEU 2.9 9.2 - - - +
20D ARG* 3.6 11.2 - - + -
21D PHE* 5.2 0.7 - - - -
29D GLN* 1.3 77.9 - - - +
31D VAL* 1.3 65.3 + - - +
32D THR* 3.9 0.9 - - - -
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Residues in contact with VAL 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 4.2 17.9 - - + -
208C ALA* 5.2 2.0 - - + -
209C HIS 3.7 12.6 - - - +
210C HIS* 3.9 17.5 - - + +
17D VAL 3.5 1.0 - - - +
18D ASP* 3.3 1.3 - - - +
19D LEU* 2.7 70.3 + - + +
21D PHE* 5.5 1.6 - - + -
30D HIS* 1.3 80.0 - - - +
32D THR* 1.3 71.3 + - - +
33D ILE* 3.9 8.7 + - + -
67D LEU* 4.0 17.0 - - + -
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Residues in contact with THR 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLN* 2.5 33.4 + - - +
192C ARG* 4.3 0.2 + - - -
208C ALA* 3.3 0.9 - - - +
209C HIS* 2.9 61.8 + - - +
16D PHE* 3.6 29.2 - - + -
17D VAL 3.3 11.0 - - - +
18D ASP* 2.7 14.0 + - + +
30D HIS* 3.9 0.3 - - - -
31D VAL* 1.3 72.6 - - - +
33D ILE* 1.3 72.9 + - - +
34D PRO* 4.4 0.4 - - - +
84D THR* 5.6 0.9 - - - -
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C GLU 3.4 12.3 - - - +
208C ALA* 3.1 27.4 - - + -
16D PHE* 3.4 4.9 - - - -
17D VAL* 2.6 46.1 + - + +
19D LEU* 4.6 19.7 - - + -
31D VAL* 4.5 11.2 - - + -
32D THR* 1.3 82.1 - - - +
34D PRO* 1.3 73.5 - - - +
37D GLN* 3.6 15.5 - - + -
38D VAL* 4.0 19.1 - - + -
42D PHE* 5.5 4.0 - - + -
47D LYS* 5.0 15.7 - - + +
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Residues in contact with PRO 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C GLU* 4.8 2.2 - - - +
206C VAL* 3.2 35.0 - - + +
207C GLU 3.2 21.8 - - - +
208C ALA* 4.0 2.7 - - - +
15D LYS 3.7 8.7 - - - +
16D PHE* 3.9 15.7 - - + -
32D THR 4.4 0.4 - - - +
33D ILE* 1.3 95.8 - - - +
35D ALA* 1.3 66.6 + - - +
36D HIS* 3.5 26.9 - - + +
37D GLN* 2.9 17.3 + - + -
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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