Contacts of the strand formed by residues 28 - 34 (chain I) in PDB entry 1F1H
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20I ARG* 3.1 28.6 + - + -
21I PHE 3.3 10.3 - - - +
27I LYS* 1.3 78.3 - - - +
29I GLN* 1.3 67.5 + - - +
88I ARG* 2.5 36.4 + - - +
236I GLN* 3.2 43.9 - - - +
237I ILE* 5.1 2.1 + - - +
240I TYR* 3.9 10.8 - - - +
181J PRO* 3.7 1.7 - - - +
182J VAL* 3.2 42.0 + - + +
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Residues in contact with GLN 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ARG* 3.2 7.8 - - - +
21I PHE* 2.5 63.4 + - + +
23I ASP* 3.7 22.2 + - + +
27I LYS* 2.8 39.2 + - - +
28I GLU* 1.3 78.4 + - - +
30I HIS* 1.3 66.1 + - - +
54I ILE* 4.6 6.3 - - + +
179J TYR 2.6 28.9 - - - +
180J PHE* 2.8 21.1 - - + +
181J PRO* 3.2 5.9 - - - +
182J VAL* 4.0 1.7 - - - +
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Residues in contact with HIS 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ASP* 2.8 40.4 - - - +
19I LEU 3.1 12.1 - - - +
20I ARG* 3.8 5.6 - - + -
21I PHE* 5.0 1.6 - - - -
29I GLN* 1.3 80.8 - - - +
31I VAL* 1.3 63.0 + - - +
32I THR* 4.0 1.6 - - - -
80I PHE* 4.8 0.4 - + - -
180J PHE* 3.1 42.9 + - - +
181J PRO 3.7 13.1 + - - -
182J VAL* 3.9 8.2 - - + -
183J PRO* 4.1 14.4 - - + +
186J ASP* 3.0 23.3 + - - -
189J GLN* 2.9 27.4 + - - -
192J ARG* 3.7 4.1 + - - -
210J HIS* 4.5 2.3 - - - +
211J HIS* 5.6 3.1 - - + -
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Residues in contact with VAL 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL 4.0 0.3 - - - +
18I ASP* 3.5 0.6 - - - +
19I LEU* 2.8 54.0 + - + +
21I PHE* 5.2 2.5 - - + -
30I HIS* 1.3 78.3 - - - +
32I THR* 1.3 69.0 + - - +
33I ILE* 4.5 8.7 - - + -
47I LYS* 4.8 9.9 - - - +
67I LEU* 4.0 19.1 - - + -
180J PHE* 4.0 16.4 - - + -
208J ALA* 4.6 3.6 - - + -
209J HIS 3.8 11.7 - - - +
210J HIS* 3.9 20.4 - - + +
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Residues in contact with THR 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I PHE* 3.6 29.6 - - + -
17I VAL 3.4 11.9 - - - +
18I ASP* 2.6 21.5 + - + +
30I HIS* 4.0 0.9 - - - -
31I VAL* 1.3 72.5 - - - +
33I ILE* 1.3 66.3 + - - +
84I THR* 5.5 0.2 - - - +
1491I MPD 4.7 0.4 - - - -
189J GLN* 3.0 18.7 + - - +
192J ARG* 5.0 0.2 + - - -
208J ALA* 3.1 6.1 - - - +
209J HIS* 2.6 72.1 + - + +
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Residues in contact with ILE 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I PHE* 3.5 3.0 - - - +
17I VAL* 2.7 50.5 + - + +
19I LEU* 4.4 21.5 - - + -
31I VAL* 4.5 4.7 - - + -
32I THR* 1.3 79.3 - - - +
34I PRO* 1.3 71.8 - - + +
37I GLN* 3.9 15.5 - - + +
38I VAL* 4.5 8.5 - - + -
42I PHE* 5.6 6.3 - - + -
47I LYS* 4.3 24.7 - - + +
207J GLU 3.0 13.7 - - - +
208J ALA* 3.1 29.4 - - + -
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Residues in contact with PRO 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I LYS 3.7 8.1 - - - +
16I PHE* 3.9 15.0 - - + -
32I THR 4.5 0.2 - - - +
33I ILE* 1.3 96.4 - - - +
35I ALA* 1.3 66.5 + - - +
36I HIS* 3.5 26.7 - - + +
37I GLN* 3.1 16.7 + - + +
200J GLU* 4.6 3.4 - - - +
206J VAL* 3.1 39.7 - - + +
207J GLU 3.2 21.8 - - - +
208J ALA* 4.0 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