Contacts of the strand formed by residues 29 - 35 (chain A) in PDB entry 4FGU
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 HIS 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LYS* 1.3 105.0 + - + +
30A TRP* 1.3 62.1 + - - +
61A ILE* 3.7 26.0 - - + +
65A GLN* 2.8 34.8 + - - +
140A HIS* 3.4 24.2 - + - +
281A MET 4.7 1.5 + - - -
282A GLN* 2.8 48.0 + - + +
283A PHE 5.6 2.0 - - - +
285A GLY* 4.7 12.8 - - - -
287A LYS* 6.1 6.2 - - + +
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS 4.1 7.0 - - - +
29A HIS* 1.3 77.4 - - - +
31A VAL* 1.3 67.5 + - - +
64A GLU 3.6 21.3 - - - -
65A GLN* 3.5 31.2 - - + -
131A LYS* 4.2 7.9 - - + -
132A VAL 4.2 9.9 - - - -
133A LEU* 3.8 28.5 - - + -
134A LYS* 4.0 36.3 - - + -
135A SER* 3.4 23.6 - - - -
139A ASP* 3.2 31.7 + - + -
140A HIS 3.0 10.6 + - - +
141A VAL* 3.4 10.3 - - + -
142A PHE* 3.0 25.3 + - - +
283A PHE 5.0 0.5 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 1.3 81.4 - - - +
32A VAL* 1.3 69.6 + - - +
33A ILE* 3.9 18.8 - - + -
56A ILE* 3.7 29.4 - - + -
61A ILE* 4.3 16.6 - - + -
65A GLN 3.1 10.0 + - - +
66A ILE* 3.5 13.3 - - + +
67A VAL* 3.1 24.6 + - - +
133A LEU* 4.9 1.1 - - - +
142A PHE* 3.2 23.6 - - + +
144A TYR 5.8 0.2 - - - +
283A PHE 3.7 21.5 - - - +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 1.3 77.8 - - - +
33A ILE* 1.3 65.0 + - - +
34A VAL* 4.0 21.3 - - + -
67A VAL* 3.4 31.4 - - + +
69A MET* 5.2 2.9 - - - -
113A PHE* 4.4 10.5 - - + -
116A VAL* 3.8 12.3 - - + -
117A LEU* 4.4 1.1 - - + -
133A LEU* 3.8 30.7 - - + -
141A VAL* 5.5 0.2 - - + -
142A PHE 3.1 6.3 + - - +
143A ILE* 3.3 18.3 - - + +
144A TYR* 2.9 27.4 + - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.9 17.0 - - + -
32A VAL* 1.3 76.2 - - - +
34A VAL* 1.3 66.8 + - - +
35A ALA 4.4 0.2 - - - -
49A ALA* 3.8 33.0 - - + +
52A ALA* 3.9 22.0 - - + +
53A TYR* 4.1 17.0 - - - +
56A ILE* 4.6 3.1 - - + -
66A ILE* 4.4 10.8 - - + -
67A VAL 3.1 6.3 + - - +
68A VAL* 3.2 27.3 - - + +
69A MET 2.8 24.9 + - - -
142A PHE* 6.3 0.2 - - + -
144A TYR* 3.7 26.9 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 4.0 7.6 - - + -
33A ILE* 1.3 83.9 - - - +
35A ALA* 1.3 67.7 + - - +
36A GLY 4.0 0.2 - - - -
69A MET* 3.5 30.3 - - + +
108A VAL* 4.4 4.3 - - + -
113A PHE* 3.7 31.9 - - + -
144A TYR 2.9 14.3 + - - +
145A PHE* 3.3 13.3 - - + -
146A THR* 3.0 27.0 + - - -
156A PHE* 3.6 30.3 - - + -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE 4.4 0.2 - - - -
34A VAL* 1.3 73.0 - - - +
36A GLY* 1.3 58.9 + - - +
37A SER 3.3 11.0 + - - +
45A HIS* 3.6 25.4 - - + +
46A GLN* 3.9 20.6 - - + +
49A ALA* 3.9 12.9 - - + +
69A MET 3.0 20.1 + - - +
70A MET* 4.0 9.7 - - + -
71A TYR 4.3 2.4 + - - -
108A VAL* 4.4 4.3 - - - +
146A THR* 3.3 10.5 - - - +
157A PRO* 5.2 0.9 - - - +
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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