Contacts of the strand formed by residues 52 - 59 (chain B) in PDB entry 1FO4
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 THR 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR* 4.4 4.9 + - - +
49B GLY* 2.6 24.5 + - - -
50B ALA 3.4 1.7 - - - +
51B CYS* 1.3 80.7 - - - +
53B VAL* 1.3 73.9 + - - +
69B SER* 4.0 8.7 - - - -
70B ALA 3.5 7.2 - - - -
71B ASN* 4.4 0.2 + - - -
87B THR* 5.7 0.2 - - - -
118B PRO 5.2 0.7 - - - -
119B GLY* 3.4 18.0 - - - +
122B MET* 3.6 23.1 - - + +
123B SER* 3.7 17.3 - - - +
146B ASN* 3.6 1.0 + - - -
341B GLN* 2.9 34.9 + - + +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.8 21.8 - - + -
30B LEU* 4.1 11.2 - - + -
39B THR* 4.0 16.6 - - + +
51B CYS 3.6 9.0 - - - +
52B THR* 1.3 83.4 - - - +
54B MET* 1.3 61.4 + - - +
55B LEU* 4.1 17.5 - - + -
69B SER* 3.3 7.8 - - - -
70B ALA* 3.1 35.7 + - + +
72B ALA* 4.0 12.3 - - + +
85B VAL* 4.3 4.0 - - + -
86B THR 3.7 10.5 - - - +
87B THR* 4.4 7.0 - - + -
122B MET* 4.3 7.4 - - - -
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 1.3 74.8 - - - +
55B LEU* 1.3 73.0 + - - +
56B SER* 3.5 19.3 - - - +
67B HIS* 3.9 23.3 - - + +
68B PHE 3.5 13.9 - - - +
84B ALA 3.8 0.3 - - - +
85B VAL* 3.5 4.2 - - - +
86B THR* 2.8 49.9 + - - +
122B MET* 4.0 13.8 - - + +
125B TYR* 3.7 32.3 - - + +
126B THR* 3.6 24.5 - - - +
129B ARG* 4.0 16.2 - - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.5 3.4 - - + -
53B VAL* 4.1 11.7 - - + -
54B MET* 1.3 80.2 - - - +
56B SER* 1.3 61.6 + - - +
67B HIS* 3.4 2.9 - - - -
68B PHE* 2.8 68.6 + - + +
70B ALA* 3.8 23.3 - - + -
75B ALA* 5.5 4.9 - - + -
80B LEU* 4.0 22.4 - - + -
83B VAL* 4.1 11.9 - - + -
84B ALA 3.4 1.6 - - - -
85B VAL* 3.5 31.2 - - + -
345B VAL* 5.2 2.5 - - + -
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B MET* 3.5 13.2 - - - +
55B LEU* 1.3 75.6 - - - +
57B LYS* 1.3 66.1 + - - +
65B ILE* 4.3 0.2 - - - -
66B ILE 3.2 6.1 - - - -
67B HIS* 2.6 34.2 + - - -
83B VAL* 3.5 3.2 - - - +
84B ALA* 2.8 39.1 + - - -
86B THR* 4.8 2.0 + - - -
212B PHE* 3.7 20.4 - - - -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B SER* 1.3 77.7 - - - +
58B TYR* 1.3 68.1 + - - +
59B ASP* 3.6 4.1 + - - +
65B ILE* 3.3 2.9 - - - +
66B ILE* 2.8 60.4 + - + +
68B PHE* 4.1 21.9 - - + -
82B HIS 4.5 12.1 - - - +
83B VAL* 4.6 16.2 - - + -
212B PHE* 3.7 14.5 - - - -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LYS* 1.3 80.5 - - - +
59B ASP* 1.3 66.5 + - - +
60B ARG* 3.1 57.0 + - + -
63B ASP* 2.9 34.6 + - - -
64B LYS* 3.7 16.6 - - - -
65B ILE* 3.6 21.6 - - + +
82B HIS 5.6 0.4 + - - -
212B PHE* 4.0 8.4 - - + -
216B LEU 5.6 1.1 - - - +
217B LEU* 4.7 3.6 - - + -
220B LYS* 3.6 51.5 + - + -
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LYS* 3.6 4.2 + - - +
58B TYR* 1.3 76.4 - - - +
60B ARG* 1.3 55.5 + - - +
61B LEU* 3.8 10.1 + - - +
62B GLN* 3.0 46.4 + - + +
63B ASP* 2.7 30.1 + - - -
64B LYS 2.7 22.3 + - - +
66B ILE* 3.8 26.9 - - + +
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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