Contacts of the strand formed by residues 43 - 55 (chain A) in PDB entry 1F5J
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 ASN 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.8 16.5 - - + -
19A LYS* 3.2 4.0 - - - +
20A ASP* 3.0 41.7 + - - +
21A THR 4.6 0.3 - - - +
41A ILE* 4.4 0.9 - - - -
42A ASN* 1.3 87.2 - - - +
44A ALA* 1.3 65.2 + - - +
45A LEU* 3.9 7.7 - - - +
125A ARG* 5.2 7.1 + - - -
180A GLU* 3.2 28.2 + - - +
181A GLY 3.0 17.9 + - - -
182A TYR* 4.1 14.9 - - + +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP 3.2 10.3 - - - +
19A LYS* 3.9 11.2 - - + -
24A THR* 3.9 18.6 - - + -
38A TRP* 5.0 0.4 - - + -
41A ILE* 4.0 17.2 - - + +
43A ASN* 1.3 79.5 - - - +
45A LEU* 1.3 64.7 + - - +
46A PHE* 4.4 13.9 - - + -
179A VAL 4.0 0.5 - - - +
180A GLU* 3.3 5.4 - - - +
181A GLY 2.9 30.6 + - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU 3.8 1.3 - - - +
17A LEU* 3.6 2.9 - - - -
18A TRP* 2.7 57.5 + - + +
43A ASN* 3.9 12.6 - - - +
44A ALA* 1.3 80.6 - - - +
46A PHE* 1.3 66.4 + - - +
47A ARG* 4.3 15.2 + - - +
81A TYR* 3.6 42.4 - - + +
90A GLU* 4.9 1.1 - - - +
92A TYR* 4.6 0.7 - - - +
178A CYS* 4.0 12.3 - - - -
179A VAL 3.5 3.8 - - - -
180A GLU* 3.7 34.5 - - + +
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU 3.6 4.3 - - - -
17A LEU* 3.7 26.2 - - + -
24A THR* 3.8 24.2 - - + -
25A THR 3.8 14.1 - - - -
26A MET* 3.8 16.6 - - + -
34A PHE* 3.7 10.7 - - + -
36A CYS* 3.5 36.1 - - + -
37A GLN 3.8 17.0 - - - -
38A TRP* 3.7 28.0 - + + -
44A ALA* 4.4 13.7 - - + -
45A LEU* 1.3 75.8 - - - +
47A ARG* 1.3 62.6 + - - +
178A CYS* 3.3 1.6 - - - -
179A VAL* 2.9 42.5 + - + +
181A GLY 5.8 0.7 - - - -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 4.7 2.4 - - + -
15A TYR* 3.2 2.9 - - - -
16A GLU* 2.9 82.8 + - + +
18A TRP* 4.6 5.9 - - - +
26A MET* 3.7 4.2 - - - +
34A PHE* 4.2 2.9 - - - -
45A LEU* 4.4 17.2 - - - +
46A PHE* 1.3 75.3 - - - +
48A THR* 1.3 68.1 + - - +
81A TYR* 3.5 30.4 + - - -
83A TRP* 4.5 5.9 - - - +
131A ILE* 4.9 4.9 - - - +
174A GLN* 3.0 36.0 + - - +
176A THR* 3.3 24.0 - - + +
177A LEU 3.3 13.7 - - - +
178A CYS* 3.6 9.6 - - + -
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 4.6 2.5 - - + -
14A TYR 3.0 10.1 - - - -
15A TYR* 3.9 17.3 - - + -
26A MET* 4.0 3.8 - - + -
28A VAL* 4.7 7.0 - - + -
32A GLY* 2.7 33.9 + - - +
34A PHE* 3.3 33.2 - - + -
47A ARG* 1.3 79.1 - - - +
49A GLY* 1.3 58.3 + - - +
176A THR* 3.7 4.9 - - - -
177A LEU 2.9 25.2 + - - -
193A ASN* 3.1 13.5 + - - -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.5 16.9 - - - -
14A TYR* 2.8 32.9 + - - -
48A THR* 1.3 76.6 - - - +
50A LYS* 1.3 67.5 + - - +
175A ILE 3.4 11.9 - - - -
176A THR* 3.8 5.1 - - - +
195A PHE* 3.8 11.2 - - - -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 2.9 31.5 + - - +
13A TYR* 4.1 29.7 - - - -
14A TYR* 4.9 3.6 - - - -
49A GLY* 1.3 79.0 - - - +
51A LYS* 1.3 65.1 + - - +
52A TYR* 3.4 22.8 - - + +
174A GLN* 3.3 4.1 - - - +
175A ILE 3.0 31.0 + - - +
176A THR* 4.5 0.8 - - - +
195A PHE* 3.6 30.5 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.7 45.9 + - + +
50A LYS* 1.3 79.4 - - - +
52A TYR* 1.3 68.1 + - - +
173A ASP* 3.4 21.9 + - - +
174A GLN* 4.0 23.6 - - + +
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS* 3.4 31.4 - - + +
51A LYS* 1.3 79.2 - - - +
53A ASN* 1.3 73.6 + - - +
54A GLN* 3.3 12.0 + - + +
59A LEU* 3.9 20.9 - - + -
62A ILE* 3.6 26.3 - - + +
172A ILE* 3.6 17.5 - - + +
173A ASP 2.9 10.5 + - - -
174A GLN* 4.3 2.0 - - - -
175A ILE* 3.7 32.5 - - + +
195A PHE* 3.2 28.6 - - - -
197A GLN* 4.0 18.7 + - - +
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 1.3 77.7 - - - +
54A GLN* 1.3 58.0 + - - +
171A THR* 3.6 17.3 - - - +
172A ILE 2.7 17.3 + - - -
173A ASP* 3.9 7.1 + - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 4.0 9.9 - - + +
53A ASN* 1.3 78.5 - - - +
55A ASN* 1.3 69.4 + - - +
56A TRP 3.3 0.3 + - - -
58A SER* 3.0 44.3 + - - +
59A LEU* 3.7 21.5 - - + +
171A THR* 3.4 5.4 - - - +
172A ILE* 2.9 28.8 + - - +
197A GLN* 4.9 5.3 + - - +
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Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 1.3 76.7 - - - +
56A TRP* 1.3 70.8 + - - +
57A GLN* 2.8 37.9 + - - +
58A SER* 3.1 25.1 + - - +
59A LEU* 3.6 6.8 - - - +
169A LEU 5.5 0.4 + - - -
170A GLY* 3.6 20.0 + - - -
171A THR* 4.2 8.2 + - - +
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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