Contacts of the strand formed by residues 47 - 54 (chain A) in PDB entry 1UJT
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 GLY 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.0 29.8 - - - +
46A GLN* 1.3 82.5 - - - +
48A TYR* 1.3 66.3 + - - -
70A LYS 4.7 1.8 - - - -
71A VAL 4.1 9.0 - - - -
72A PRO* 4.1 15.9 - - - -
95A TYR* 3.5 16.7 + - - +
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Residues in contact with TYR 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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17A VAL* 5.4 0.2 - - - +
19A VAL* 4.8 0.4 - - + -
36A TRP* 3.8 44.2 - + + -
38A VAL* 3.6 21.6 - - + +
41A GLN* 5.4 0.7 - - - +
42A PRO* 4.3 8.3 - - - +
45A ILE* 3.8 13.3 - - + +
47A GLY* 1.3 82.9 - - - -
49A ARG* 1.3 59.7 + - - +
50A VAL* 3.9 1.7 + - + +
67A LEU 3.5 2.6 - - - +
68A ASP* 3.8 0.2 - - - -
69A ALA* 3.0 37.3 + - + +
70A LYS 4.6 0.4 - - - +
71A VAL 4.1 6.5 - - - -
72A PRO* 4.3 16.3 + - + -
74A GLU 4.0 7.9 - - - -
75A ARG* 3.4 29.8 + - - -
92A VAL* 4.2 6.7 - - + -
93A ARG 4.0 4.0 - - - +
94A PRO* 3.6 36.8 - - + -
95A TYR* 3.3 13.0 - - - -
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Residues in contact with ARG 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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48A TYR* 1.3 70.8 - - - +
50A VAL* 1.3 60.6 + - - +
51A MET* 3.5 11.6 + - + +
66A ASN* 4.1 35.4 - - + +
67A LEU 4.1 5.8 - - - +
68A ASP* 5.2 4.6 - - - +
91A LYS 3.9 1.0 - - - +
93A ARG* 3.1 43.6 + - + +
95A TYR* 3.3 45.2 - - + -
97A ASN 3.9 13.5 + - - -
98A GLU* 3.6 25.2 + - - +
100A GLN* 4.0 16.8 - - - +
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Residues in contact with VAL 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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34A VAL* 4.6 10.1 - - + -
36A TRP* 4.1 21.1 - - + -
48A TYR* 4.9 3.8 - - + +
49A ARG* 1.3 71.1 - - - +
51A MET* 1.3 61.2 + - - +
52A TYR* 3.7 8.1 - - - -
67A LEU* 3.1 36.6 + - + +
69A ALA* 5.8 1.1 - - + -
77A ALA* 3.6 26.9 - - + -
79A LEU* 3.9 17.5 - - + -
90A ILE* 3.5 27.8 - - + -
91A LYS 4.0 5.4 - - - +
92A VAL* 4.3 8.3 - - + -
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Residues in contact with MET 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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49A ARG* 3.5 14.4 + - + +
50A VAL* 1.3 74.0 - - - +
52A TYR* 1.3 59.8 + - - +
64A TRP* 3.6 45.4 - - + -
65A GLN 3.1 12.8 - - - +
66A ASN* 3.4 23.1 - - + +
90A ILE* 3.1 18.5 - - - +
91A LYS* 3.2 36.2 + - + +
93A ARG* 3.6 29.4 - - - +
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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 VAL 3.7 9.6 - - - -
51A MET* 1.3 74.9 - - - +
53A ARG* 1.3 63.7 + - - +
64A TRP* 3.5 2.9 - - - -
65A GLN* 2.8 89.5 + - + +
66A ASN 4.4 4.9 - - - -
67A LEU* 4.5 11.5 - - + +
79A LEU* 3.4 48.9 - - + -
80A VAL 4.5 7.7 + - - -
81A ASN* 5.6 1.2 - - - +
82A LEU* 3.8 30.1 - - + -
88A TYR* 5.0 3.8 - + + -
89A GLU 3.4 6.3 - - - -
90A ILE* 3.6 10.8 - - + -
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Residues in contact with ARG 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 79.2 - - - +
54A GLN* 1.3 73.6 + - - +
55A THR* 4.9 5.3 - - + +
59A GLN 5.8 0.9 - - - +
61A THR* 3.3 41.7 + - - +
62A SER 5.0 0.2 - - - +
63A SER 4.1 7.2 - - - +
64A TRP* 2.6 80.7 - - + +
65A GLN* 3.9 10.5 - - - +
88A TYR* 3.1 15.2 - - - -
89A GLU* 3.1 30.3 + - - +
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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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53A ARG* 1.3 83.8 + - - +
55A THR* 1.3 64.2 + - - +
57A GLY* 3.2 27.8 - - - +
58A LEU 3.3 1.2 - - - +
59A GLN* 3.2 35.0 + - + +
60A ALA* 3.2 24.9 - - - +
61A THR 3.3 7.6 + - - -
65A GLN* 5.2 0.2 - - - +
83A LYS* 3.2 15.2 - - - +
86A VAL* 3.2 35.1 - - + +
87A THR 3.9 0.2 - - - -
88A TYR* 2.5 39.5 + - + -
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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