Contacts of the strand formed by residues 49 - 56 (chain G) in PDB entry 5FLX
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 VAL 49 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35G GLU* 3.2 28.5 - - - +
36G VAL 3.9 13.5 - - - +
37G ALA* 5.3 6.7 - - + -
38G ALA 4.7 0.4 - - - +
47G GLY 3.7 8.2 + - - +
48G TYR* 1.3 78.9 - - - +
50G VAL* 1.3 58.9 + - - +
113G ILE* 3.2 2.5 - - - +
114G VAL* 2.5 59.4 + - + +
115G LYS* 5.0 2.7 - - + +
116G LYS* 4.4 7.4 + - + +
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Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G PHE* 5.8 3.6 - - + -
34G THR 4.2 0.5 - - - +
35G GLU* 5.1 0.3 - - - -
36G VAL* 3.0 40.1 + - + +
38G ALA* 4.1 13.9 - - + +
41G LEU* 5.1 3.8 - - + -
45G TRP* 3.8 29.4 - - + -
48G TYR 4.4 0.2 + - - -
49G VAL* 1.3 81.2 - - - +
51G ARG* 1.3 76.4 + - - +
52G ILE* 5.8 0.4 - - + -
111G LEU* 3.6 28.0 - - + -
112G VAL 3.3 20.0 - - - +
113G ILE* 4.0 11.9 - - + -
114G VAL* 4.6 0.2 - - - -
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Residues in contact with ARG 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17471 C 5.7 3.2 + - - -
33G ALA* 5.0 14.6 - - - +
34G THR 3.9 15.3 - - - +
35G GLU* 5.3 5.4 + - - +
50G VAL* 1.3 74.1 - - - +
52G ILE* 1.3 66.1 - - - +
53G SER* 3.6 3.6 + - - +
111G LEU* 3.6 1.9 - - - -
112G VAL* 2.4 58.0 + - + +
113G ILE 5.5 1.8 - - - -
114G VAL* 3.7 34.4 - - + +
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Residues in contact with ILE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G PHE* 4.7 19.3 - - + +
30G LYS* 3.8 31.9 - - + +
31G ARG 4.7 7.9 - - - +
32G MET* 3.5 8.3 - - - +
33G ALA* 2.8 36.3 + - - +
34G THR 4.4 5.2 + - - +
36G VAL* 4.0 19.3 - - + -
50G VAL* 5.8 0.7 - - + -
51G ARG* 1.3 73.1 - - - +
53G SER* 1.3 60.3 + - - +
54G GLY* 3.9 21.3 - - - +
63G MET* 6.0 2.2 - - - -
102G VAL* 5.3 15.0 - - + -
109G LEU* 5.7 7.0 - - + -
110G ASN 3.7 4.9 - - - +
111G LEU* 4.5 14.8 - - + -
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Residues in contact with SER 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641 A 4.8 0.2 + - - -
1651 G 3.3 51.1 - - - +
1661 A 3.6 8.7 + - - -
32G MET* 3.4 14.2 - - - +
33G ALA* 5.5 2.0 - - - +
51G ARG* 3.6 3.9 + - - +
52G ILE* 1.3 72.0 - - - +
54G GLY* 1.3 57.5 + - - +
110G ASN* 3.5 10.8 + - - -
112G VAL* 3.3 29.0 - - - +
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Residues in contact with GLY 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641 A 5.0 5.6 - - - -
32G MET* 3.5 19.6 - - - -
52G ILE* 3.4 12.7 - - - +
53G SER* 1.3 79.7 - - - +
55G GLY* 1.3 58.9 + - - -
63G MET* 4.6 3.4 - - - -
109G LEU* 3.8 3.2 - - - +
110G ASN* 2.8 36.7 + - - +
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Residues in contact with GLY 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641 A 5.6 1.2 + - - -
54G GLY* 1.3 74.3 - - - -
56G ASN* 1.3 72.1 + - - +
61G PHE 3.9 1.4 - - - +
62G PRO* 3.5 15.1 - - - +
63G MET* 3.5 25.0 + - - +
106G LEU* 4.7 4.3 - - - -
108G VAL 3.3 11.7 - - - -
109G LEU* 4.2 10.1 - - - -
110G ASN* 4.4 3.2 - - - +
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Residues in contact with ASN 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1551 G 3.8 27.1 + - - +
1561 G 4.4 15.5 + - - +
1641 A 4.0 15.9 - - - +
55G GLY* 1.3 82.8 - - - +
57G ASP* 1.3 65.2 + - - +
60G GLY* 4.6 5.8 - - - -
61G PHE 3.9 2.7 - - - -
62G PRO* 3.4 23.0 - - - +
106G LEU* 3.7 6.7 - - - +
107G SER 3.0 21.8 + - - -
108G VAL* 2.7 42.8 + - + +
110G ASN* 5.3 4.0 + - - -
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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