Contacts of the strand formed by residues 59 - 69 (chain C) in PDB entry 1FL7
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 CYS 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C CYS* 3.5 7.6 - - - -
58C THR* 1.3 78.1 - - - +
60C CYS* 1.3 65.2 + - - +
61C VAL* 3.0 9.4 + - + +
84C CYS* 3.3 0.3 - - - -
85C SER 2.7 30.9 + - - +
87C CYS* 2.0 50.0 - - + -
34D THR* 3.9 11.4 - - - +
48D GLN* 3.6 38.8 - - - +
49D LYS 4.6 5.6 - - - -
50D THR* 5.2 0.4 - - - -
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Residues in contact with CYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C CYS* 2.0 52.9 - - + -
28C CYS* 3.6 4.3 - - - -
29C MET* 3.2 35.9 - - - -
30C GLY 3.9 7.2 - - - +
32C CYS* 3.3 7.3 - - - -
59C CYS* 1.3 71.0 - - - +
61C VAL* 1.3 62.9 + - - +
83C HIS 4.0 0.2 - - - -
34D THR* 3.4 24.2 + - - +
35D ARG 4.1 3.1 + - - -
36D ASP* 3.6 17.2 + - - +
48D GLN* 4.2 2.3 + - - -
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C CYS* 3.8 5.6 - - - -
59C CYS* 3.0 19.6 + - + +
60C CYS* 1.3 82.2 - - - +
62C ALA* 1.3 66.7 + - - +
82C CYS* 3.6 1.0 - - - -
83C HIS* 3.0 34.4 + - + +
85C SER* 3.7 16.6 - - - +
86C THR 3.6 17.3 - - - +
88C TYR 5.7 1.3 - - - +
90C HIS* 3.7 23.8 - - + +
91C LYS* 4.0 6.5 - - + -
36D ASP* 3.6 18.6 - - - +
48D GLN* 4.3 7.2 - - - +
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C CYS* 3.4 12.7 - - - -
61C VAL* 1.3 72.5 - - - +
63C LYS* 1.3 63.5 + - - +
64C SER 3.8 10.3 - - - +
65C TYR* 4.2 10.4 - - + -
77C GLU* 4.8 0.2 - - - +
79C HIS* 3.4 39.9 - - + +
81C ALA 3.5 0.2 - - - -
83C HIS* 4.4 0.2 - - - -
90C HIS* 4.4 10.8 + - + -
91C LYS* 3.7 15.8 - - - +
36D ASP* 2.9 14.5 + - - +
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL 3.4 2.0 + - - -
62C ALA* 1.3 74.0 - - - +
64C SER* 1.3 62.8 + - - +
65C TYR* 5.6 0.2 - - - -
81C ALA* 2.8 34.5 + - + +
82C CYS 4.5 3.8 + - - +
83C HIS* 3.7 45.2 - - + +
90C HIS* 5.1 5.4 + - - -
91C LYS* 4.6 8.1 - - + +
92C SER* 6.0 0.5 - - - -
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA* 3.3 5.6 - - - +
63C LYS* 1.3 80.1 - - - +
65C TYR* 1.3 72.9 + - - +
79C HIS* 3.7 2.1 - - - -
80C THR* 2.6 38.3 + - - -
81C ALA* 3.7 14.3 + - - +
90C HIS* 6.2 0.2 - - - -
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 5.5 4.3 + - - -
62C ALA* 4.2 9.9 - - + -
64C SER* 1.3 83.8 - - - +
66C ASN* 1.3 75.1 + - - +
67C ARG* 4.2 21.6 + - + -
77C GLU* 3.4 47.0 + - + -
78C ASN 3.6 15.9 - - - +
79C HIS* 3.7 12.3 - - + -
80C THR* 3.7 5.6 + - - -
90C HIS* 3.8 32.2 + + - -
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Residues in contact with ASN 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TYR* 1.3 86.2 + - - +
67C ARG* 1.3 68.9 + - - +
68C VAL* 4.9 2.9 - - + -
77C GLU* 3.4 2.1 - - - -
78C ASN* 2.8 43.9 + - + +
80C THR* 3.8 19.0 - - - +
1I NAG 5.1 1.4 - - - +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TYR* 4.2 19.4 + - + -
66C ASN* 1.3 78.5 - - - +
68C VAL* 1.3 68.5 + - - +
75C LYS* 4.4 40.5 + - + +
76C VAL* 4.0 3.0 - - - +
77C GLU* 3.5 35.8 + - - +
38D VAL 5.2 0.8 + - - -
40D LYS* 5.7 3.4 - - - +
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 4.4 8.5 - - + -
66C ASN* 4.3 4.5 - - + +
67C ARG* 1.3 86.8 - - - +
69C THR* 1.3 77.1 + - - +
70C VAL* 4.2 9.2 - - + -
75C LYS* 3.1 7.6 - - - +
76C VAL* 2.9 39.3 + - - +
78C ASN* 4.3 18.4 - - + +
1I NAG 4.1 31.4 - - + +
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL* 1.3 79.9 - - - +
70C VAL* 1.3 70.4 + - - +
73C GLY* 3.6 25.1 - - - +
74C PHE 3.5 1.3 - - - -
75C LYS* 3.8 26.2 - - + +
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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