Contacts of the strand formed by residues 66 - 74 (chain X) 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 ILE 66 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6151 C 4.5 11.2 + - - +
6161 A 2.7 34.6 + - - +
6171 G 4.4 7.1 + - - -
56X GLY* 4.9 3.8 - - - -
57X VAL 3.6 13.0 - - - +
58X GLU* 4.2 16.4 - - - +
65X ALA* 1.3 77.7 - - - +
67X ARG* 1.3 69.2 + - - +
68X LYS* 3.8 8.1 + - + +
4e GLY* 3.9 34.5 - - - +
5e SER 4.7 5.6 - - - +
6e LEU* 6.0 2.7 - - + -
8e ARG* 3.7 26.0 - - - +
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Residues in contact with ARG 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6171 G 3.0 46.2 + - - -
6181 C 3.0 39.3 + - - +
6191 A 4.0 5.5 - - - +
56X GLY* 3.2 5.5 - - - -
57X VAL* 3.0 51.4 + - + +
59X ALA* 4.8 13.0 - - + -
65X ALA* 4.5 7.9 - - - +
66X ILE* 1.3 76.4 + - - +
68X LYS* 1.3 61.6 + - - +
69X CYS* 3.6 0.7 + - - -
84X PHE* 3.6 29.0 - - + -
114X ASP* 2.4 32.1 + - - -
115X ILE* 3.7 19.3 - - + +
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Residues in contact with LYS 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6161 A 4.1 8.0 + - - -
6171 G 3.2 40.2 + - - +
56X GLY* 4.6 3.4 - - - -
66X ILE* 4.4 7.4 - - + +
67X ARG* 1.3 72.7 - - - +
69X CYS* 1.3 59.8 + - - +
84X PHE* 3.8 10.5 - - - -
85X VAL* 3.3 37.6 + - + +
87X ASN 5.7 0.2 - - - +
91X LEU* 3.5 35.7 - - + +
5e SER 4.4 3.4 + - - -
6e LEU* 4.0 27.7 + - + +
8e ARG 2.7 29.7 + - - -
9e ALA* 3.7 10.9 - - - +
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Residues in contact with CYS 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X LYS* 3.9 3.5 - - - +
55X VAL 2.9 40.1 + - - +
56X GLY* 4.3 0.2 - - - -
57X VAL* 3.6 31.4 - - + -
67X ARG 3.6 1.3 + - - -
68X LYS* 1.3 78.8 - - - +
70X VAL* 1.3 70.9 + - - +
82X THR* 5.4 3.1 - - - -
83X ALA 3.1 10.5 - - - +
84X PHE* 4.2 13.7 - - - +
91X LEU* 5.2 2.1 - - - +
115X ILE* 4.7 0.4 - - - -
118X VAL* 3.5 29.8 - - + -
6e LEU* 5.8 0.9 - - - +
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Residues in contact with VAL 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X VAL* 3.6 40.8 - - + -
53X GLU 3.9 3.4 - - - +
54X LYS* 4.2 14.8 - - + -
69X CYS* 1.3 81.4 - - - +
71X ARG* 1.3 66.7 + - - +
72X VAL* 3.6 7.3 + - + -
82X THR* 3.5 2.2 - - - -
83X ALA* 2.6 49.0 + - + +
85X VAL* 3.8 24.5 - - + -
91X LEU* 4.4 7.6 - - + -
94X ILE* 4.7 9.2 - - + -
100X VAL* 5.1 3.1 - - + -
122X VAL* 5.2 2.2 - - + -
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Residues in contact with ARG 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17131 C 5.8 5.7 + - - -
51X VAL* 3.6 5.5 - - - -
52X LEU* 3.0 53.9 + - + -
53X GLU* 2.6 51.5 + - + +
55X VAL* 5.2 8.3 - - + +
69X CYS 4.4 0.2 - - - -
70X VAL* 1.3 70.2 - - - +
72X VAL* 1.3 61.3 + - - +
80X LYS* 4.0 34.5 - - + +
81X ILE 3.5 8.3 - - - +
82X THR* 4.5 20.6 - - + +
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Residues in contact with VAL 72 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48X LYS 5.2 0.2 - - - -
49X GLY* 3.7 30.7 - - - +
50X ILE 3.6 2.7 - - - +
51X VAL* 5.4 0.7 - - + -
52X LEU 5.2 0.2 - - - -
70X VAL* 3.8 21.3 - - + +
71X ARG* 1.3 79.5 - - - +
73X GLN* 1.3 64.5 + - - +
74X LEU* 4.7 10.3 - - + +
79X LYS 3.8 1.2 - - - +
80X LYS* 3.4 5.6 - - - -
81X ILE* 2.5 49.5 + - + +
83X ALA* 3.8 19.3 - - + -
100X VAL* 4.4 12.8 - - + +
102X VAL* 4.3 16.6 - - + -
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Residues in contact with GLN 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X GLY* 3.2 2.8 - - - -
50X ILE* 2.8 42.0 + - + +
52X LEU* 4.9 15.1 - - + +
72X VAL* 1.3 75.0 - - - +
74X LEU* 1.3 69.7 + - - +
75X ILE* 3.7 3.0 + - + +
78X GLY* 2.8 43.0 + - - -
79X LYS 3.8 2.6 - - - +
80X LYS* 3.3 31.5 - - + +
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Residues in contact with LEU 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X PRO* 4.2 12.1 - - + -
41X PHE* 3.9 19.1 - - + +
47X ALA* 4.2 12.1 - - + -
48X LYS 4.3 8.5 - - - +
72X VAL* 4.9 8.5 - - + -
73X GLN* 1.3 83.2 + - - +
75X ILE* 1.3 64.1 + - - +
76X LYS* 4.2 2.0 - - + +
77X ASN* 3.7 28.0 - - + +
78X GLY* 3.4 26.9 - - - +
79X LYS* 3.3 25.7 + - + +
81X ILE* 3.6 29.2 - - + -
102X VAL* 5.4 1.8 - - + -
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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