Contacts of the strand formed by residues 29 - 37 (chain A) in PDB entry 1U3H
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLN 4.1 22.4 - - - -
3A VAL* 4.8 1.3 - - + -
24A TYR* 3.7 31.8 + + + -
26A ASN* 2.7 47.8 + - + +
27A SER 3.9 6.9 - - - +
28A ALA* 1.3 78.0 - - - +
30A ASP* 1.3 59.2 + - - +
31A TYR 3.9 0.2 - - - -
32A PHE* 3.6 26.4 - - + -
51A SER* 4.2 6.6 - - - -
66A PHE* 5.3 0.3 - - - -
68A LYS* 5.8 1.4 - - - +
92A ALA* 3.8 27.1 - - + -
93A SER* 3.3 25.8 - - - +
98A ALA* 3.6 4.7 - - + -
105A ARG* 4.5 23.8 - - + -
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Residues in contact with ASP 30 (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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28A ALA 3.3 4.2 + - - +
29A PHE* 1.3 75.1 - - - +
31A TYR* 1.3 68.5 + - - +
32A PHE* 3.6 5.4 - - - -
50A LEU* 3.4 14.6 - - + +
51A SER* 2.8 41.0 + - - +
93A SER* 3.0 14.6 + - - +
98A ALA 3.1 13.0 - - - +
99A ASN* 4.0 15.3 - - + +
73D ALA* 6.2 0.3 - - - +
74D GLU* 6.1 0.9 - - - +
77D THR* 3.8 27.4 + - + +
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Residues in contact with TYR 31 (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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30A ASP* 1.3 89.4 + - - +
32A PHE* 1.3 70.8 + - - +
33A PRO* 3.2 35.0 - - + +
45A LEU* 4.3 10.2 - - - +
48A SER* 3.4 30.6 + - - -
49A ILE 3.6 10.3 - - - -
50A LEU* 4.2 16.4 - - + -
92A ALA* 3.2 4.9 - - - +
93A SER* 3.0 41.9 + - - +
104A GLN* 4.3 4.5 - - + -
99B GLY 3.8 5.4 - - - -
100B GLY* 3.3 43.9 + - - -
104B TYR 4.1 1.3 - - - -
105B GLU* 4.4 7.8 + - - +
70D ARG* 4.7 7.7 + - - -
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Residues in contact with PHE 32 (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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22A CYS* 6.0 0.4 - - - -
24A TYR* 3.2 36.6 - + - -
29A PHE* 3.6 24.7 - - + -
30A ASP* 3.6 21.3 - - - -
31A TYR* 1.3 75.6 - - - +
33A PRO* 1.3 63.6 - - - +
34A TRP* 4.0 7.1 + - - +
48A SER* 3.5 2.0 - - - -
49A ILE* 3.0 41.8 + - + +
51A SER* 4.4 2.9 - - - -
66A PHE* 3.3 33.7 - + - -
73A LEU* 3.8 30.1 - - + -
90A CYS* 5.4 0.9 - - - -
91A ALA 3.4 9.6 - - - +
92A ALA* 3.6 22.9 - - + -
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Residues in contact with PRO 33 (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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31A TYR* 3.2 39.5 - - + +
32A PHE* 1.3 87.3 - - - +
34A TRP* 1.3 61.9 + - - +
35A TYR* 3.6 6.6 - - + +
45A LEU* 3.3 18.8 - - + -
48A SER* 3.8 7.4 - - - -
89A PHE 3.7 0.5 - - - +
91A ALA* 3.1 36.2 + - + +
92A ALA* 4.1 1.6 - - - +
104A GLN* 3.5 26.5 - - - +
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Residues in contact with TRP 34 (chain A).
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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5A GLN* 4.2 9.4 - - - -
20A LEU* 4.0 23.1 - - + -
21A ASN 4.3 6.1 - - - -
22A CYS* 3.8 15.5 - - + -
32A PHE* 4.0 4.9 + - - +
33A PRO* 1.3 77.5 - - - +
35A TYR* 1.3 63.0 + - - +
45A LEU* 3.6 3.1 - - - +
46A LEU* 2.8 29.8 + - + +
47A ILE* 2.9 17.3 + - + +
64A ILE* 3.5 31.3 - - + +
73A LEU* 3.9 23.9 - - + +
74A SER 4.3 0.4 - - - -
75A LEU* 3.6 57.2 - - + -
88A TYR* 4.6 7.2 - - + -
89A PHE 3.0 15.0 - - - -
90A CYS* 3.7 33.1 - - + -
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Residues in contact with TYR 35 (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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33A PRO* 3.6 23.8 - - + +
34A TRP* 1.3 80.2 - - - +
36A GLN* 1.3 59.8 + - - +
37A GLN 4.2 0.2 - - - -
43A PRO* 4.0 13.5 - - + -
44A ALA* 3.0 10.1 - - - +
45A LEU* 3.5 27.6 - - + -
46A LEU* 5.0 0.4 - - - -
87A THR 4.0 0.3 - - - +
88A TYR* 3.4 7.0 - - - +
89A PHE* 2.7 46.5 + - + +
91A ALA* 4.4 0.4 - - + -
104A GLN* 2.8 30.9 + - - -
106A PHE* 3.6 21.5 - + + -
105B GLU* 4.0 1.7 - - - -
106B GLN* 3.0 47.9 + - + +
108B PHE* 3.7 20.9 - + - -
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Residues in contact with GLN 36 (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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35A TYR* 1.3 73.1 - - - +
37A GLN* 1.3 61.9 + - - +
38A PHE* 3.3 46.4 + - + -
42A GLY 4.3 1.0 - - - +
43A PRO* 3.7 1.1 - - - -
44A ALA* 2.6 37.6 + - + +
46A LEU* 4.2 28.4 - - + +
62A PHE* 5.0 2.9 - - - -
84A ASP* 4.7 3.1 - - - +
86A ALA* 5.1 0.9 - - + -
88A TYR* 2.9 46.7 + - + -
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Residues in contact with GLN 37 (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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35A TYR 4.2 0.2 - - - -
36A GLN* 1.3 73.4 - - - +
38A PHE* 1.3 58.1 + - - +
39A PRO* 4.0 1.9 - - + -
41A GLU 3.0 28.6 + - - +
42A GLY 3.8 4.9 - - - +
43A PRO* 3.4 29.1 - - + +
86A ALA* 2.4 28.0 - - - +
87A THR* 2.8 29.3 + - - +
89A PHE* 3.7 10.6 - - + -
37B GLN* 3.0 29.1 + - - +
91B PHE* 3.1 28.1 - - - -
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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