Contacts of the strand formed by residues 50 - 63 (chain D) 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 THR 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C SER* 3.5 9.0 - - - -
55C SER* 3.6 16.2 - - - +
57C SER* 3.2 39.0 + - - -
87C CYS* 5.0 2.4 - - - -
32D CYS* 3.7 9.6 - - - -
48D GLN 4.1 4.0 + - - -
49D LYS* 1.3 80.7 + - - +
51D CYS* 1.3 81.6 + - - +
52D THR* 3.2 10.9 + - + +
85D GLY 2.9 28.3 + - - -
87D CYS* 5.1 10.7 - - - +
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Residues in contact with CYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C SER* 2.8 32.3 + - - +
35C ARG* 3.8 14.2 - - - +
55C SER* 4.3 0.2 + - - -
3D CYS* 2.0 59.5 - - + -
28D CYS* 4.1 3.4 - - - -
29D ALA* 3.5 29.4 - - - -
30D GLY 4.2 2.9 - - - +
32D CYS* 3.5 5.7 - - - -
50D THR* 1.3 82.1 - - - +
52D THR* 1.3 64.2 + - - +
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Residues in contact with THR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ALA* 4.0 12.4 - - - +
53C VAL* 5.5 0.2 - - - +
55C SER* 4.9 7.2 - - - -
28D CYS* 3.6 14.1 - - - -
50D THR* 3.2 22.0 - - - +
51D CYS* 1.3 81.2 - - - +
53D PHE* 1.3 95.8 + - - +
83D HIS* 3.0 36.9 + - + +
85D GLY 4.0 10.5 - - - +
86D LYS 4.3 10.8 - - - +
87D CYS* 5.1 5.9 - - - -
88D ASP 5.7 1.3 + - - +
92D THR* 5.0 3.8 + - - +
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Residues in contact with PHE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA* 4.4 2.0 - - - +
53C VAL* 3.9 11.0 - - + -
27D TRP* 3.6 31.0 - + + -
28D CYS* 3.5 11.4 - - - +
52D THR* 1.3 94.1 + - - +
54D LYS* 1.3 66.7 + - - +
55D GLU 3.9 7.0 - - - +
56D LEU* 3.4 44.2 - - + -
79D ALA* 4.4 7.2 - - + -
81D GLN 3.5 7.6 - - - +
83D HIS* 3.6 8.2 - - - -
88D ASP* 4.6 11.0 - - + -
91D SER* 3.3 21.1 - - - -
92D THR* 3.5 21.8 - - - -
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D THR 3.6 0.2 + - - -
53D PHE* 1.3 81.1 - - - +
55D GLU* 1.3 76.0 + - + +
81D GLN* 2.6 47.2 + - - +
83D HIS* 3.3 48.4 + - + +
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 4.0 2.1 - - - -
54D LYS* 1.3 96.4 - - + +
56D LEU* 1.3 57.6 + - - +
79D ALA* 4.1 0.7 - - - -
80D THR* 2.7 49.2 + - + +
81D GLN* 3.0 19.4 + - + +
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 3.8 24.0 - - + -
27D TRP* 4.0 5.6 - - + -
53D PHE* 3.4 41.5 - - + -
55D GLU* 1.3 77.8 + - - +
57D VAL* 1.3 73.7 + - - +
58D TYR* 4.8 14.1 - - + +
77D PRO* 4.2 9.2 - - + -
78D VAL 3.2 17.0 - - - +
79D ALA* 4.3 2.0 - - - -
80D THR* 3.5 1.3 - - - -
91D SER* 6.0 1.3 - - - -
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 1.3 76.3 - - - +
58D TYR* 1.3 74.4 + - - +
59D GLU* 4.6 8.5 - - + +
77D PRO* 3.3 2.8 - - - +
78D VAL* 2.5 56.3 + - + +
79D ALA 6.0 0.2 - - - -
80D THR* 3.0 24.5 - - + +
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Residues in contact with TYR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 2.7 29.3 + - - +
53C VAL* 5.5 0.3 - - - +
56D LEU* 4.8 15.5 - - + +
57D VAL* 1.3 86.6 - - - +
59D GLU* 1.3 68.1 + - - +
75D THR* 4.2 18.8 - - - -
76D TYR* 3.5 6.5 - - - -
77D PRO* 3.7 34.5 - - + +
1H NAG 2.4 42.6 + - - -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D VAL* 4.6 8.3 - - + +
58D TYR* 1.3 79.2 - - - +
60D THR* 1.3 66.1 + - - +
75D THR* 2.9 3.6 - - - -
76D TYR* 2.7 63.6 + - + +
78D VAL* 3.8 24.4 - - + +
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 1.3 75.4 - - - +
61D VAL* 1.3 75.4 + - - +
73D LEU* 3.9 37.9 - - + -
74D TYR 3.3 10.1 - - - +
75D THR* 2.8 25.8 - - + +
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 5.1 9.0 - - + -
21D ILE* 5.8 2.5 - - + -
23D ILE* 3.3 20.2 - - + -
60D THR* 1.3 85.7 - - - +
62D ARG* 1.3 74.2 + - - +
63D VAL* 3.3 11.2 + - + +
73D LEU* 3.4 1.0 - - - -
74D TYR* 2.9 30.1 + - + +
76D TYR* 3.3 30.1 - - + +
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 5.5 0.2 - - - +
61D VAL* 1.3 80.8 - - - +
63D VAL* 1.3 63.5 + - - +
64D PRO* 3.9 3.5 - - - +
71D ASP* 3.2 29.5 + - + +
72D SER 3.1 7.6 - - - +
73D LEU* 3.3 25.9 - - + +
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 3.6 31.0 - - + +
14D LYS* 4.4 21.5 - - + +
19D PHE* 5.2 0.4 - - + -
21D ILE* 3.4 20.0 - - + -
61D VAL* 3.9 4.5 - - + +
62D ARG* 1.3 73.8 - - - +
64D PRO* 1.3 87.9 - - + +
71D ASP* 3.1 5.7 - - - +
72D SER* 2.7 39.9 + - - +
73D LEU 5.0 0.4 - - - -
74D TYR* 3.7 20.6 - - + +
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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