Contacts of the strand formed by residues 19 - 35 (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 PHE 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLU* 3.8 1.2 - - - +
14D LYS* 2.8 47.1 + - + +
17D CYS* 3.3 36.1 - - + +
18D ARG* 1.3 77.8 - - - +
20D CYS* 1.3 70.5 + - - +
21D ILE* 4.4 11.2 - - + -
63D VAL* 5.2 0.4 - - + -
64D PRO* 3.9 31.4 - - + -
65D GLY 4.0 13.2 - - - -
66D CYS* 5.7 0.4 - - + -
104D CYS* 5.1 0.2 - - - -
106D PHE* 3.6 11.2 - - - -
107D GLY 5.7 4.7 - - - +
108D GLU 5.8 6.1 - - - -
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Residues in contact with CYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA* 4.7 4.3 - - + -
12D ILE 2.9 15.0 - - - +
13D GLU* 3.5 31.6 - - - -
19D PHE* 1.3 80.8 - - - +
21D ILE* 1.3 65.0 + - - +
103D TYR 4.9 1.6 - - - -
104D CYS* 2.0 55.6 - - + -
106D PHE* 4.3 0.7 - - - -
108D GLU 4.9 9.8 + - - +
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Residues in contact with ILE 21 (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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11D ALA* 3.6 2.8 - - - -
12D ILE* 2.7 66.4 + - + +
19D PHE* 4.4 12.1 - - + -
20D CYS* 1.3 79.7 - - - +
22D SER* 1.3 58.4 + - - +
61D VAL* 5.8 2.7 - - + -
62D ARG 5.5 0.2 - - - +
63D VAL* 3.4 34.8 - - + -
64D PRO* 3.7 26.5 - - + -
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D THR* 5.0 9.4 - - - -
10D ILE 3.6 13.9 - - - -
11D ALA* 5.1 2.2 - - - -
12D ILE* 4.5 2.1 - - - +
21D ILE* 1.3 79.3 - - - +
23D ILE* 1.3 61.2 + - - +
102D SER* 6.6 0.2 - - - -
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Residues in contact with ILE 23 (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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9D THR* 3.7 3.5 - - - -
10D ILE* 3.2 43.6 + - + +
12D ILE* 3.3 28.3 - - + -
22D SER* 1.3 76.2 - - - +
24D ASN* 1.3 73.4 + - - +
61D VAL* 3.3 29.2 - - + -
76D TYR* 2.8 35.7 - - + +
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Residues in contact with ASN 24 (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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7D ASN* 3.0 34.9 + - - +
8D ILE 3.3 14.6 + - - +
9D THR* 3.6 20.3 - - + +
23D ILE* 1.3 86.0 - - - +
25D THR* 1.3 80.3 + - - +
76D TYR* 4.6 1.9 + - - -
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Residues in contact with THR 25 (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* 4.7 0.2 - - + -
7D ASN* 3.9 0.7 - - - -
8D ILE* 2.8 36.4 + - + +
10D ILE* 3.7 36.6 - - + +
23D ILE* 4.5 1.1 - - - -
24D ASN* 1.3 89.1 + - - +
26D ALA* 1.3 60.9 + - - +
27D TRP* 3.8 17.3 - - + +
76D TYR* 3.8 10.8 - - - -
78D VAL* 3.4 30.6 - - - +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 4.5 12.8 - - + -
6D THR 3.6 10.1 - - - +
7D ASN* 4.0 2.8 + - - +
25D THR* 1.3 73.8 + - - +
27D TRP* 1.3 64.7 + - - +
78D VAL* 3.6 8.7 - - + +
79D ALA* 3.0 36.5 + - - +
1J NAG 3.3 25.5 + - - +
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Residues in contact with TRP 27 (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* 3.6 32.1 - - + +
37C TYR* 3.8 6.3 - - - -
38C PRO* 3.3 25.2 - - + +
53C VAL* 3.3 43.3 - - + -
5D LEU* 3.4 2.9 - - - -
6D THR* 2.7 39.0 + - - +
8D ILE* 3.9 15.9 - - + -
25D THR* 3.7 15.3 + - + -
26D ALA* 1.3 84.6 - - - +
28D CYS* 1.3 67.8 + - - +
53D PHE* 3.6 34.3 - + + -
56D LEU* 4.0 5.6 - - + -
77D PRO* 2.9 39.2 + - + -
78D VAL* 3.6 4.6 - - - +
79D ALA* 3.6 15.0 - - + -
82D CYS* 4.0 1.8 - - - -
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Residues in contact with CYS 28 (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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35C ARG* 3.2 1.2 - - - +
36C ALA* 2.9 33.3 + - + +
6D THR* 4.2 0.2 - - - -
8D ILE* 5.8 0.9 - - - +
27D TRP* 1.3 81.5 - - - +
29D ALA* 1.3 66.6 + - - +
51D CYS* 4.1 4.0 - - - -
52D THR* 3.8 19.7 - - - -
53D PHE* 3.5 23.3 - - - +
79D ALA* 4.0 8.7 - - - -
82D CYS* 2.0 56.3 - - + -
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 4.0 12.3 - - + -
34C SER 3.6 8.1 - - - -
35C ARG* 3.7 12.8 - - + -
4D GLU* 3.1 31.6 + - - +
6D THR* 3.5 21.4 + - + +
8D ILE* 5.7 3.1 - - + -
28D CYS* 1.3 78.6 - - - +
30D GLY* 1.3 60.0 + - - +
51D CYS* 3.5 9.1 - - - -
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Residues in contact with GLY 30 (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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33C PHE* 3.3 16.7 - - - -
34C SER* 3.1 33.0 + - - +
3D CYS* 3.6 11.2 - - - -
4D GLU* 4.5 3.1 - - - -
29D ALA* 1.3 76.4 - - - +
31D TYR* 1.3 69.4 + - - -
51D CYS* 3.6 3.0 - - - -
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Residues in contact with TYR 31 (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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7C CYS* 4.0 28.4 - - + -
31C CYS* 4.2 8.7 - - + -
32C CYS* 3.4 26.5 - - - -
33C PHE* 3.6 33.5 - + + +
3D CYS 3.2 17.5 + - - +
30D GLY* 1.3 77.5 - - - -
32D CYS* 1.3 72.4 + - - +
84D CYS* 3.3 6.6 - - - -
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Residues in contact with CYS 32 (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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7C CYS* 4.1 2.2 - - - -
30C GLY 3.7 0.3 - - - +
31C CYS* 3.1 22.5 - - - -
32C CYS* 3.1 13.8 + - - +
34C SER* 4.4 1.6 - - - +
3D CYS* 3.9 1.3 - - - -
31D TYR* 1.3 80.1 - - - +
33D TYR* 1.3 65.9 + - - +
34D THR* 3.8 4.9 + - + +
49D LYS* 4.8 5.2 - - + +
50D THR* 3.7 9.0 - - - +
51D CYS* 3.5 31.4 - - - +
84D CYS* 2.0 51.1 - - + -
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Residues in contact with TYR 33 (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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7C CYS* 4.0 3.2 - - - -
8C PRO* 4.1 22.0 - - + -
13C GLN* 5.4 0.3 - - - +
29C MET* 2.8 29.8 - - + +
30C GLY* 3.1 28.0 - - - -
31C CYS* 3.7 21.8 - - - -
32D CYS* 1.3 74.5 - - - +
34D THR* 1.3 69.9 + - - +
35D ARG* 3.2 33.7 - - - -
49D LYS* 4.8 8.7 - - - +
84D CYS* 5.1 0.6 - - - +
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Residues in contact with THR 34 (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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29C MET* 3.3 2.4 - - - +
30C GLY 2.7 31.7 + - - +
32C CYS* 4.8 2.1 + - - +
58C THR 4.8 1.4 + - - -
59C CYS* 3.9 10.3 - - - -
60C CYS* 3.4 27.8 + - - +
32D CYS* 3.9 8.0 + - + +
33D TYR* 1.3 82.7 - - - +
35D ARG* 1.3 62.3 + - - +
48D GLN* 3.3 39.5 - - + -
49D LYS* 3.9 18.6 - - + +
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Residues in contact with ARG 35 (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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27C GLN* 4.5 9.2 - - - +
28C CYS 3.4 5.6 - - - +
29C MET* 3.4 28.4 - - + +
60C CYS 4.1 4.9 - - - -
33D TYR* 3.2 31.9 - - - -
34D THR* 1.3 75.9 - - - +
36D ASP* 1.3 59.6 + - - +
37D LEU* 3.7 28.9 + - + +
46D LYS* 4.0 22.4 + - - +
48D GLN* 3.5 18.1 + - - +
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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