Contacts of the strand formed by residues 51 - 57 (chain A) in PDB entry 1FXT
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 LYS 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A THR* 3.8 8.1 - - - +
25A GLU* 2.8 36.6 + - - -
38A THR* 3.1 33.7 - - - +
39A PHE 3.7 4.3 - - - +
40A LEU* 4.9 9.4 - - + -
50A GLY* 1.3 70.3 - - - -
52A PHE* 1.3 58.5 + - - +
53A VAL* 3.4 14.5 + - + +
73A THR* 3.4 15.1 + - - -
148A TYR 4.3 0.5 - - - +
149A ALA* 3.6 11.9 + - - -
150A SER 3.3 21.9 + - - +
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Residues in contact with PHE 52 (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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37A GLY 3.7 1.9 - - - +
38A THR* 3.4 18.8 - - - -
39A PHE* 2.9 41.9 + + + +
41A GLY* 3.6 15.5 - - - -
42A PRO* 4.6 1.1 - - + -
47A TYR* 3.3 38.6 - - + -
50A GLY* 3.5 12.3 - - - -
51A LYS* 1.3 68.0 - - - +
53A VAL* 1.3 60.5 + - - +
54A VAL* 3.7 6.1 + - - +
71A PHE* 3.9 8.5 - + + -
73A THR* 4.1 6.7 - - + -
75A VAL* 3.7 33.7 - - + -
113A LEU* 3.6 20.4 - - + -
145A THR* 4.0 14.1 - - + -
149A ALA* 3.6 23.6 - - + -
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Residues in contact with VAL 53 (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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25A GLU* 5.5 1.8 - - - +
36A LYS* 4.0 18.4 - - + -
38A THR* 4.0 23.1 - - + -
51A LYS* 3.7 26.5 - - + +
52A PHE* 1.3 70.8 - - - +
54A VAL* 1.3 61.9 + - - +
71A PHE* 3.2 9.9 - - - -
72A ASP* 3.2 46.7 + - + +
73A THR* 3.4 19.2 + - - +
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Residues in contact with VAL 54 (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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35A LEU 3.3 3.1 - - - +
36A LYS* 3.4 3.6 - - - -
37A GLY 2.9 48.1 + - - +
39A PHE* 4.5 1.3 - - + -
52A PHE 4.0 3.4 - - - +
53A VAL* 1.3 73.8 - - - +
55A ASP* 1.3 62.1 + - - +
56A ILE* 3.6 9.4 - - + +
69A MET* 3.8 33.0 - - + -
70A GLN 3.9 13.2 - - - +
71A PHE* 3.6 36.1 - - + +
72A ASP* 4.3 0.9 - - - -
87A ILE* 4.7 2.0 - - + -
106A LEU* 4.0 5.2 - - + -
109A LEU* 3.9 15.5 - - + -
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Residues in contact with ASP 55 (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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27A VAL* 3.7 7.6 - - - +
34A HIS* 3.3 28.7 + - - -
35A LEU 3.6 3.1 - - - -
36A LYS* 2.7 34.7 + - - +
54A VAL* 1.3 69.8 - - - +
56A ILE* 1.3 62.8 + - - +
68A LYS 3.0 5.1 - - - +
70A GLN* 3.0 71.1 + - + +
72A ASP* 3.7 6.6 + - - +
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Residues in contact with ILE 56 (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 HIS 3.4 8.6 - - - +
34A HIS* 3.5 9.3 + - - -
35A LEU* 2.9 34.1 + - + +
37A GLY* 3.9 28.0 - - - +
54A VAL* 3.6 13.2 - - + +
55A ASP* 1.3 81.8 - - - +
57A GLU* 1.3 58.9 + - - +
58A VAL* 3.8 20.0 - - + +
67A PRO* 3.8 23.3 - - + -
68A LYS 3.7 3.1 - - - -
69A MET* 4.4 15.0 - - + -
102A LEU* 4.3 15.5 - - + -
106A LEU* 3.9 25.1 - - + -
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Residues in contact with GLU 57 (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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3A ARG* 2.9 37.2 + - - -
33A HIS* 3.4 17.5 + - - +
34A HIS* 3.9 19.7 + - + +
55A ASP* 5.2 0.4 + - - -
56A ILE* 1.3 71.0 - - - +
58A VAL* 1.3 56.1 + - - +
59A PRO* 3.2 26.6 - - + +
60A MET* 4.0 5.7 + - - +
68A LYS* 2.9 52.3 + - + +
70A GLN* 5.7 2.1 - - - +
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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