Contacts of the strand formed by residues 5 - 13 (chain A) in PDB entry 3U53
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 ALA 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ARG* 1.3 75.3 - - - +
6A CYS* 1.3 66.4 + - - +
42A LYS* 4.6 4.9 - - + -
43A GLY* 3.0 26.7 - - - +
44A HIS* 4.2 10.5 - - + +
45A VAL 4.5 0.4 - - - +
90A THR 2.9 12.1 + - - +
91A VAL* 3.1 21.0 - - + -
92A ILE* 2.9 22.2 + - - +
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Residues in contact with CYS 6 (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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4A ARG* 5.1 1.3 - - - -
5A ALA* 1.3 80.7 - - - +
7A GLY* 1.3 59.8 + - - +
42A LYS* 3.2 5.4 - - - -
43A GLY 2.8 27.8 + - - +
45A VAL* 4.2 9.2 - - - -
51A ASP* 3.5 58.1 - - - +
54A THR* 3.8 10.3 - - - +
55A ALA* 3.9 11.0 - - + +
58A GLU* 4.1 3.1 - - - +
91A VAL* 4.6 0.2 - - - -
92A ILE* 3.2 20.0 - - + +
94A TRP* 4.6 1.1 - - + -
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Residues in contact with GLY 7 (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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6A CYS* 1.3 76.6 - - - +
8A LEU* 1.3 74.8 + - - +
41A PRO 3.1 15.0 - - - -
42A LYS* 3.8 6.0 - - - +
55A ALA* 3.4 12.1 - - - +
92A ILE 2.8 9.3 + - - +
93A TYR* 3.4 12.0 - - - -
94A TRP* 3.3 14.2 + - - -
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Residues in contact with LEU 8 (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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7A GLY* 1.3 83.3 - - - +
9A ILE* 1.3 60.7 + - - +
10A ILE* 3.1 17.2 + - + +
40A PRO* 3.2 15.2 - - - +
41A PRO* 3.1 16.7 + - - +
52A LEU* 4.4 0.2 - - + -
55A ALA* 3.7 19.3 - - + +
56A LEU* 4.1 13.2 - - + -
59A THR* 3.4 23.9 + - + +
70A LEU* 3.9 25.8 - - + -
72A ILE* 3.9 13.5 - - + -
93A TYR* 3.6 4.2 - - - -
94A TRP* 3.4 30.7 - - + +
96A ALA* 3.9 13.2 - - + -
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Residues in contact with ILE 9 (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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8A LEU* 1.3 70.0 - - - +
10A ILE* 1.3 60.2 + - - +
26A PHE* 3.8 29.8 - - + -
40A PRO* 4.0 13.0 - - + -
76A PHE* 4.4 16.2 - - + -
78A ARG* 5.6 0.2 - - + -
93A TYR* 3.9 32.5 - - + -
94A TRP 2.8 12.0 + - - +
95A LEU* 3.5 16.5 - - + +
96A ALA 3.0 23.0 + - - +
131A MET* 5.6 1.1 - - - -
134A ALA* 4.1 30.7 - - + +
135A LEU* 4.0 18.6 - - + -
138A GLY* 5.4 1.6 - - - -
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Residues in contact with ILE 10 (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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8A LEU* 3.1 16.6 + - + +
9A ILE* 1.3 74.7 - - - +
11A PHE* 1.3 61.8 + - - +
26A PHE* 3.3 7.6 - - - +
27A LEU* 3.0 43.0 + - + +
40A PRO* 4.7 3.0 - - - +
41A PRO* 4.0 17.9 - - + -
59A THR* 4.1 15.5 - - + -
65A ILE* 4.3 4.5 - - + -
70A LEU* 3.4 31.0 - - + -
96A ALA* 3.5 14.6 - - + +
98A VAL* 3.6 23.6 - - + -
116A TRP* 3.8 13.9 - - + -
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Residues in contact with PHE 11 (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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10A ILE* 1.3 76.4 - - - +
12A ARG* 1.3 72.5 + - - +
13A ARG* 4.2 17.3 - - + -
24A ILE* 4.2 7.4 - - + -
25A GLU 2.9 13.2 - - - +
26A PHE* 3.8 17.7 - - + -
73A ILE* 4.0 11.9 - - + -
95A LEU* 3.5 24.0 - - + -
96A ALA 3.0 35.7 + - - -
97A GLU* 3.4 36.0 - - + -
98A VAL* 3.0 25.7 + - - +
116A TRP* 3.7 4.7 - - - -
142A LEU* 3.6 35.7 - - + -
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Residues in contact with ARG 12 (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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11A PHE* 1.3 76.7 - - - +
13A ARG* 1.3 64.3 + - - +
14A CYS* 4.0 4.7 + - - -
24A ILE* 3.3 5.7 - - - -
25A GLU* 2.7 64.7 + - + +
97A GLU* 5.1 0.2 - - - -
98A VAL* 3.3 23.8 - - + +
101A TYR* 2.9 68.6 + - + -
116A TRP* 3.3 54.4 - - + +
159A GOL 3.7 4.9 - - - +
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Residues in contact with ARG 13 (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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11A PHE* 4.2 12.2 - - + -
12A ARG* 1.3 77.9 - - - +
14A CYS* 1.3 62.3 + - - +
15A LEU* 3.9 27.7 + - + +
23A ALA* 3.1 10.9 + - - +
24A ILE* 4.2 11.8 - - + +
73A ILE* 6.2 0.6 - - - +
97A GLU* 3.0 33.1 + - - +
101A TYR* 4.0 6.6 - - - -
142A LEU* 4.5 19.8 + - - +
146A GLU* 3.1 36.5 + - - +
159A GOL 3.1 36.1 + - - +
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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