Contacts of the strand formed by residues 28 - 34 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D PRO* 3.8 1.6 - - - +
182D VAL* 3.2 40.8 + - + +
20E ARG* 3.1 31.1 + - + -
21E PHE 3.3 9.9 - - - +
26E GLY 3.8 0.2 + - - -
27E LYS* 1.3 79.8 - - - +
29E GLN* 1.3 68.2 + - - +
88E ARG* 2.5 36.0 + - - +
236E GLN* 3.2 43.0 - - - +
237E ILE* 5.1 1.9 + - - +
240E TYR* 3.9 11.4 - - - +
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Residues in contact with GLN 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D TYR 2.7 28.1 - - - +
180D PHE* 2.9 18.6 - - + +
181D PRO* 3.1 9.0 - - - +
182D VAL* 3.8 1.7 - - - +
20E ARG* 3.2 7.4 - - - +
21E PHE* 2.5 64.0 + - + +
23E ASP* 3.7 22.1 + - + +
27E LYS* 2.8 39.6 + - - +
28E GLU* 1.3 81.3 + - - +
30E HIS* 1.3 66.3 + - - +
54E ILE* 4.6 6.6 - - + +
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Residues in contact with HIS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 3.0 43.2 + + - +
181D PRO 3.6 14.4 + - - -
182D VAL* 3.6 12.0 - - + -
183D PRO* 3.9 15.8 - - + +
186D ASP* 3.0 22.6 + - - -
189D GLN* 3.0 26.7 + - - -
192D ARG* 3.8 4.3 + - - -
210D HIS* 4.7 2.3 - - - +
211D HIS* 5.6 2.8 + - + -
18E ASP* 2.8 39.9 - - - +
19E LEU 3.1 12.3 - - - +
20E ARG* 3.8 2.5 - - + -
21E PHE* 5.0 1.8 - - - -
29E GLN* 1.3 79.1 - - - +
31E VAL* 1.3 61.5 + - - +
32E THR* 4.0 1.6 - - - -
80E PHE* 4.8 0.7 - + - -
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 4.0 17.7 - - + -
208D ALA* 4.8 3.1 - - + -
209D HIS 3.8 11.9 - - - +
210D HIS* 3.9 20.0 - - + +
17E VAL 4.0 0.3 - - - +
18E ASP* 3.5 1.4 - - - +
19E LEU* 2.8 52.6 + - + +
21E PHE* 5.2 2.2 - - + -
30E HIS* 1.3 78.1 - - - +
32E THR* 1.3 69.3 + - - +
33E ILE* 4.5 9.6 - - + -
47E LYS* 4.8 10.3 - - - +
67E LEU* 4.0 19.3 - - + -
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Residues in contact with THR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D GLN* 2.9 20.8 + - - +
192D ARG* 5.0 0.2 + - - -
208D ALA* 3.3 4.0 - - - +
209D HIS* 2.8 69.4 + - + +
16E PHE* 3.6 29.2 - - + -
17E VAL 3.4 12.8 - - - +
18E ASP* 2.6 21.4 + - + +
30E HIS* 4.0 0.9 - - - -
31E VAL* 1.3 72.7 - - - +
33E ILE* 1.3 67.4 + - - +
34E PRO* 4.5 0.4 - - - +
84E THR* 5.5 0.2 - - - +
1487E MPD 4.7 0.4 - - - -
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Residues in contact with ILE 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D GLU 3.3 14.1 - - - +
208D ALA* 3.3 27.8 - - + -
16E PHE* 3.5 3.4 - - - +
17E VAL* 2.7 51.2 + - + +
19E LEU* 4.4 22.0 - - + -
31E VAL* 4.2 5.4 + - + -
32E THR* 1.3 79.6 - - - +
34E PRO* 1.3 71.3 - - + +
37E GLN* 3.9 15.9 - - + +
38E VAL* 4.5 8.5 - - + -
42E PHE* 5.6 4.9 - - + -
47E LYS* 4.3 24.7 - - + +
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Residues in contact with PRO 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D GLU* 4.8 2.5 - - - +
206D VAL* 3.3 37.7 - - + +
207D GLU 3.4 20.6 - - - +
208D ALA* 4.1 2.9 - - - +
15E LYS 3.7 9.6 - - - +
16E PHE* 3.9 14.1 - - + -
32E THR 4.5 0.2 - - - +
33E ILE* 1.3 96.5 - - - +
35E ALA* 1.3 66.0 + - - +
36E HIS* 3.5 26.0 - - + +
37E GLN* 3.1 16.7 + - + +
38E VAL 4.3 0.2 + - - -
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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