Contacts of the strand formed by residues 86 - 95 (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 VAL 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.2 38.6 - - + +
56A SER* 4.0 5.8 - - - -
57A GLY* 3.3 28.3 - - - +
83A LYS* 3.5 25.8 - - + +
85A GLY* 1.3 79.0 - - - +
87A THR* 1.3 67.8 + - - +
88A TYR* 3.2 19.5 - - + -
109A VAL 3.6 0.2 - - - +
110A ARG* 4.6 4.7 - - - +
111A THR* 3.0 27.2 + - - +
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Residues in contact with THR 87 (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* 3.9 0.2 - - - +
55A THR* 3.3 28.7 + - - +
56A SER* 4.4 10.9 - - - -
86A VAL* 1.3 88.0 - - - +
88A TYR* 1.3 65.8 + - - +
108A THR* 3.5 34.5 - - + +
109A VAL 3.1 13.9 - - - +
110A ARG* 4.2 17.5 + - + +
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Residues in contact with TYR 88 (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* 5.0 2.2 - + + -
53A ARG* 3.1 27.1 - - - +
54A GLN* 2.5 43.8 + - + -
59A GLN* 5.8 0.5 - - - +
65A GLN* 5.1 5.6 - - - -
82A LEU* 4.6 22.1 - - + -
83A LYS* 3.0 31.5 + - - +
86A VAL* 3.2 39.9 - - + -
87A THR* 1.3 73.0 - - - +
89A GLU* 1.3 62.0 + - - +
90A ILE* 3.7 8.4 + - + +
107A LYS 3.5 1.9 - - - +
108A THR* 3.4 3.0 - - - -
109A VAL* 2.7 51.4 + - + +
111A THR* 4.2 10.8 - - + -
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.4 3.6 - - - -
53A ARG* 3.1 34.7 + - - +
55A THR* 3.7 23.5 - - + +
64A TRP* 3.5 30.1 - - + -
88A TYR* 1.3 68.9 - - - +
90A ILE* 1.3 65.5 + - - +
91A LYS* 5.7 0.2 - - - -
106A SER* 3.3 36.0 + - - +
107A LYS 3.6 4.5 - - - +
108A THR* 4.1 17.6 - - + +
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Residues in contact with ILE 90 (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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21A LEU* 3.7 6.6 - - + +
24A PRO* 4.2 11.9 - - + -
32A VAL* 4.4 5.6 - - + -
34A VAL* 4.2 20.0 - - + -
50A VAL* 3.5 26.5 - - + -
51A MET 3.1 17.0 - - - +
52A TYR* 3.6 10.3 - - + -
79A LEU* 3.4 23.6 - - + -
82A LEU* 5.9 1.1 - - + -
88A TYR* 3.9 8.1 - - + +
89A GLU* 1.3 81.0 - - - +
91A LYS* 1.3 65.4 + - - +
106A SER* 3.4 1.0 - - - -
107A LYS* 2.9 33.8 + - - +
109A VAL* 3.9 25.1 - - + -
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Residues in contact with LYS 91 (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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21A LEU* 3.8 5.6 - - - -
49A ARG 3.9 3.1 - - - +
50A VAL* 4.0 1.0 - - - -
51A MET* 3.2 37.3 + - + +
64A TRP* 3.4 42.2 - - + -
89A GLU* 6.1 0.2 - - - -
90A ILE* 1.3 83.4 - - - +
92A VAL* 1.3 64.1 + - - +
93A ARG* 3.2 35.4 + - - +
103A ASP* 4.3 13.2 + - + +
104A SER 3.6 21.5 - - - +
106A SER* 3.9 16.4 - - - -
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Residues in contact with VAL 92 (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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19A VAL* 3.7 14.5 - - + +
21A LEU* 3.2 24.6 - - + +
34A VAL* 3.6 13.2 - - + -
36A TRP* 3.1 62.1 - - + +
48A TYR* 4.2 9.4 - - + -
49A ARG 4.5 2.5 - - - -
50A VAL* 4.3 8.3 - - + +
91A LYS* 1.3 73.0 - - - +
93A ARG* 1.3 64.2 + - - +
104A SER* 3.0 33.7 + - - +
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Residues in contact with ARG 93 (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* 4.0 4.7 - - - -
49A ARG* 3.1 43.1 + - + +
51A MET* 3.6 26.4 - - - +
91A LYS* 3.2 35.0 + - - +
92A VAL* 1.3 79.3 - - - +
94A PRO* 1.3 69.5 - - + +
100A GLN* 3.4 39.6 - - + +
101A GLY 3.7 8.2 + - - +
103A ASP* 3.6 39.8 + - - +
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Residues in contact with PRO 94 (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 LEU* 4.7 6.1 - - + +
17A VAL* 4.1 19.7 - - + +
19A VAL* 3.4 27.6 - - + -
42A PRO* 5.1 1.3 - - + -
45A ILE* 3.1 21.8 - - + -
48A TYR* 3.6 17.2 - - + -
93A ARG* 1.3 88.4 - - + +
95A TYR* 1.3 64.1 + - - +
100A GLN* 3.0 7.6 - - - +
101A GLY* 2.9 34.4 + - - -
102A MET 3.7 8.5 - - - +
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Residues in contact with TYR 95 (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 LEU* 4.6 3.3 - - - +
44A PHE* 6.1 0.2 - - - -
45A ILE* 3.2 20.8 - - - +
46A GLN* 3.3 12.2 + - + +
47A GLY* 3.5 8.4 + - - -
48A TYR* 3.3 30.7 - - - -
49A ARG* 3.3 55.2 - - + +
68A ASP* 3.9 20.1 - - + +
70A LYS* 4.1 20.8 + - - +
94A PRO* 1.3 78.6 - - - +
96A PHE* 1.3 77.7 + - - +
97A ASN 4.1 6.1 - - - -
99A PHE 3.1 18.8 - - - +
100A GLN* 3.8 9.6 - - + +
101A GLY 4.6 0.9 - - - +
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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