Contacts of the strand formed by residues 4 - 14 (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 GLU 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D CYS* 1.3 83.9 + - - +
5D LEU* 1.3 78.0 + - - +
6D THR* 3.1 23.9 + - + +
29D ALA 3.1 21.4 + - - +
30D GLY* 4.5 2.8 - - - -
82D CYS* 3.8 10.1 - - - -
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Residues in contact with LEU 5 (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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4D GLU* 1.3 79.6 - - - +
6D THR* 1.3 62.7 + - - +
26D ALA* 4.5 8.7 - - + -
27D TRP* 3.4 11.9 - - - +
79D ALA* 3.5 35.0 - - + +
80D THR 3.1 26.0 - - - +
81D GLN* 4.3 2.7 - - - -
82D CYS* 3.2 28.7 - - - +
1J NAG 6.5 0.4 - - - -
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Residues in contact with THR 6 (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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4D GLU* 3.1 26.0 - - + +
5D LEU* 1.3 75.6 - - - +
7D ASN* 1.3 65.4 + - - +
8D ILE* 3.5 10.8 + - - +
26D ALA* 3.6 3.8 - - - -
27D TRP 2.7 37.0 + - - +
29D ALA* 3.5 30.6 - - + +
1J NAG 5.0 1.8 - - - -
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Residues in contact with ASN 7 (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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6D THR* 1.3 74.2 - - - +
8D ILE* 1.3 61.8 + - - +
24D ASN* 3.0 31.5 + - - +
25D THR 3.9 8.0 - - - +
26D ALA* 4.0 0.4 + - - +
1J NAG 1.5 78.9 + - - -
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Residues in contact with ILE 8 (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 4.7 0.7 - - - +
37C TYR* 3.7 29.8 - - + -
38C PRO* 4.3 0.7 - - + -
6D THR* 3.7 22.0 - - - +
7D ASN* 1.3 80.6 - - - +
9D THR* 1.3 68.3 + - - +
10D ILE* 3.9 15.0 - - + -
24D ASN* 3.3 6.2 - - - -
25D THR* 2.8 44.8 + - + +
27D TRP* 3.9 17.9 - - + -
28D CYS 5.8 0.7 - - - +
29D ALA* 5.7 3.1 - - + -
101D PRO* 4.0 13.2 - - + -
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Residues in contact with THR 9 (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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8D ILE* 1.3 86.6 - - - +
10D ILE* 1.3 66.4 + - - +
22D SER* 5.0 8.6 - - - -
23D ILE 3.7 11.4 - - - -
24D ASN* 3.6 21.1 - - + +
101D PRO* 4.5 3.5 - - - +
102D SER* 3.6 21.7 + - - -
410D SO4 4.9 1.4 + - - -
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Residues in contact with ILE 10 (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* 3.2 52.5 - - + +
8D ILE* 3.9 9.6 + - + -
9D THR* 1.3 77.2 - - - +
11D ALA* 1.3 67.0 + - - +
12D ILE* 5.2 2.2 - - + -
22D SER* 3.6 8.1 - - - -
23D ILE* 3.2 47.6 + - + +
25D THR* 3.7 15.0 - - + +
74D TYR* 5.2 4.7 - - + +
76D TYR* 4.3 23.6 - - + -
101D PRO* 3.5 14.6 - - + +
102D SER* 4.3 1.6 - - - -
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Residues in contact with ALA 11 (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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40C PRO* 5.7 4.9 - - - +
41C LEU 5.8 1.2 + - - -
10D ILE* 1.3 82.5 - - - +
12D ILE* 1.3 63.4 + - - +
13D GLU* 3.7 4.4 + - - +
20D CYS* 4.7 11.4 - - + -
21D ILE 3.7 6.1 - - - +
22D SER* 4.6 2.0 - - - +
74D TYR* 5.0 6.4 + - - -
101D PRO 3.2 6.5 + - - +
102D SER* 3.5 19.1 - - - +
103D TYR 3.3 26.3 - - - +
104D CYS* 4.9 1.3 - - + -
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Residues in contact with ILE 12 (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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10D ILE* 5.0 0.9 - - + -
11D ALA* 1.3 71.5 - - - +
13D GLU* 1.3 64.5 + - - +
14D LYS* 3.9 1.0 + - - +
20D CYS* 2.9 5.4 - - - -
21D ILE* 2.7 66.5 + - + +
22D SER 4.5 0.4 - - - -
23D ILE* 3.3 47.1 - - + +
61D VAL* 5.1 8.1 - - + -
63D VAL* 3.6 25.4 - - + -
74D TYR* 3.1 42.4 - - + -
76D TYR* 5.5 0.2 - - + -
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Residues in contact with GLU 13 (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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41C LEU* 3.8 43.3 + - + +
42C ARG* 3.3 15.8 + - - +
11D ALA 3.7 4.9 + - - +
12D ILE* 1.3 77.5 - - - +
14D LYS* 1.3 59.6 - - - +
15D GLU* 3.5 7.6 + - - +
20D CYS* 3.5 15.0 - - - -
74D TYR* 5.2 6.8 - - - -
103D TYR* 4.6 3.8 - - - +
104D CYS* 3.7 3.1 - - - -
105D SER* 2.7 50.5 + - - -
106D PHE* 3.5 22.9 - - + -
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Residues in contact with LYS 14 (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 3.9 1.6 + - - +
13D GLU* 1.3 72.6 - - - +
15D GLU* 1.3 64.3 + - - +
16D GLU* 3.5 11.9 - - - +
17D CYS* 3.2 11.3 + - + +
18D ARG 3.1 15.9 + - - -
19D PHE* 2.8 45.4 + - + +
20D CYS* 5.7 0.2 - - - -
63D VAL* 4.1 15.1 + - + +
64D PRO 2.8 27.8 + - - +
65D GLY* 3.6 4.9 - - - -
69D HIS* 3.4 28.5 - - - -
70D ALA 3.4 17.6 + - - -
71D ASP* 4.0 1.6 - - - +
72D SER* 3.6 23.3 + - - +
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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