Contacts of the strand formed by residues 72 - 85 (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 SER 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LYS* 3.6 23.9 + - - +
62D ARG* 3.1 8.1 - - - +
63D VAL* 2.7 42.2 + - - +
69D HIS* 5.6 2.9 - - - -
70D ALA 4.6 2.0 - - - -
71D ASP* 1.3 77.1 - - - +
73D LEU* 1.3 69.6 + - - +
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Residues in contact with LEU 73 (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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60D THR* 3.9 21.8 - - + -
61D VAL 3.4 1.6 - - - -
62D ARG* 3.3 33.7 - - + -
72D SER* 1.3 85.4 + - - +
74D TYR* 1.3 64.2 + - - +
75D THR* 4.2 4.3 - - + -
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Residues in contact with TYR 74 (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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38C PRO* 6.1 1.2 - - - +
39C THR 4.8 6.1 + - - -
41C LEU* 5.4 12.4 + - + +
44C LYS* 4.1 17.1 + - - -
10D ILE* 5.2 4.3 - - + +
11D ALA 5.0 4.3 + - - -
12D ILE* 3.1 44.2 - - + -
13D GLU 5.4 5.6 - - - -
59D GLU 3.7 0.7 - - - +
60D THR* 3.3 2.0 - - - +
61D VAL* 2.9 29.4 + - + +
63D VAL* 3.7 20.6 - - + -
73D LEU* 1.3 78.3 - - - +
75D THR* 1.3 73.8 + - - +
76D TYR* 3.7 28.4 - + + +
1H NAG 5.0 7.9 - - - -
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Residues in contact with THR 75 (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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58D TYR* 4.2 15.0 - - - -
59D GLU 2.9 8.7 - - - -
60D THR* 2.8 26.9 - - + +
73D LEU* 5.4 3.4 - - + -
74D TYR* 1.3 90.5 - - - +
76D TYR* 1.3 60.7 + - - +
77D PRO* 4.8 0.3 - - - +
1H NAG 3.4 25.7 + - - +
2H NDG 3.4 27.7 + - - +
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Residues in contact with TYR 76 (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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38C PRO* 5.2 1.1 - - + -
10D ILE* 4.3 22.4 - - + -
12D ILE* 5.5 0.2 - - + -
23D ILE* 2.8 30.5 - - + +
24D ASN 4.6 2.8 + - - -
25D THR* 3.8 13.5 - - - -
58D TYR* 3.7 5.6 - - - -
59D GLU* 2.7 57.0 + - + +
61D VAL* 3.3 27.9 - - + +
74D TYR* 3.7 33.0 - + + +
75D THR* 1.3 75.3 - - - +
77D PRO* 1.3 74.9 - - + +
78D VAL* 3.3 27.0 - - + +
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Residues in contact with PRO 77 (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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38C PRO* 3.7 17.2 - - + +
44C LYS* 5.8 4.3 - - - +
52C ASN* 3.9 28.3 - - + +
53C VAL* 4.1 14.8 - - + -
25D THR* 4.6 0.2 + - - -
27D TRP* 2.9 30.5 + - + -
56D LEU* 4.2 7.4 - - + -
57D VAL 3.3 7.0 - - - +
58D TYR* 3.7 28.6 - - + -
76D TYR* 1.3 92.0 - - + +
78D VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 78 (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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25D THR* 3.4 15.7 - - - +
26D ALA* 3.6 14.1 - - + +
27D TRP* 3.6 5.2 - - - +
56D LEU* 3.2 6.1 - - - +
57D VAL* 2.5 52.1 + - + +
59D GLU* 3.8 26.5 - - + +
76D TYR* 3.3 38.6 - - + +
77D PRO* 1.3 76.1 - - - +
79D ALA* 1.3 70.6 + - - +
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Residues in contact with ALA 79 (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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5D LEU* 3.5 25.7 - - + +
26D ALA* 3.0 25.6 + - - +
27D TRP* 3.6 24.4 - - + +
28D CYS* 4.0 13.0 - - - -
53D PHE* 4.4 4.7 - - + -
55D GLU 4.1 2.9 - - - -
56D LEU* 4.3 4.0 - - - -
57D VAL* 6.0 0.2 - - - -
78D VAL* 1.3 78.8 - - - +
80D THR* 1.3 61.5 + - - +
81D GLN 4.8 0.7 - - - +
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Residues in contact with THR 80 (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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5D LEU* 3.1 19.8 - - - +
55D GLU* 2.7 32.2 + - + +
56D LEU* 3.5 2.3 - - - -
57D VAL* 3.0 32.0 - - + +
79D ALA* 1.3 73.2 - - - +
81D GLN* 1.3 59.4 + - + +
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Residues in contact with GLN 81 (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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5D LEU* 4.3 3.8 - - - -
28D CYS* 4.4 0.4 - - - -
53D PHE* 3.5 3.8 - - - +
54D LYS* 2.6 66.1 + - + +
55D GLU* 3.0 18.8 + - + +
80D THR* 1.3 84.1 - - + +
82D CYS* 1.3 70.7 + - - +
83D HIS* 5.8 0.2 - - - -
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Residues in contact with CYS 82 (chain D).
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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3D CYS* 4.3 7.6 - - - +
4D GLU* 4.1 9.6 - - - -
5D LEU* 3.2 49.3 - - - +
28D CYS* 2.0 57.0 - - + -
52D THR 3.6 0.9 - - - -
81D GLN* 1.3 85.2 - - - +
83D HIS* 1.3 66.8 + - - +
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Residues in contact with HIS 83 (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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3D CYS* 3.8 11.7 - - - -
52D THR* 3.0 32.9 + - + +
53D PHE 3.6 17.3 - - - -
54D LYS* 3.3 48.3 + - + +
82D CYS* 1.3 77.9 - - - +
84D CYS* 1.3 72.5 + - - +
85D GLY* 3.2 21.1 + - - -
86D LYS 4.9 2.7 + - - -
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Residues in contact with CYS 84 (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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3D CYS* 3.6 8.7 - - - -
31D TYR 3.3 11.2 - - - -
32D CYS* 2.0 50.7 - - + -
33D TYR 5.1 0.2 - - - -
49D LYS* 3.7 24.3 + - + +
50D THR 3.4 7.0 - - - -
83D HIS* 1.3 76.9 - - - +
85D GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 85 (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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49D LYS* 3.4 16.4 - - - -
50D THR* 2.9 29.7 + - - +
52D THR* 4.0 2.7 - - - +
83D HIS* 3.2 22.5 + - - -
84D CYS* 1.3 75.5 - - - +
86D LYS* 1.3 68.6 + - - +
87D CYS 3.5 1.2 + - - -
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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