Contacts of the strand formed by residues 97 - 102 (chain B) in PDB entry 1UEX
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 ILE 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER* 2.9 29.4 - - - -
72B HIS* 2.7 44.8 + - + +
73B PHE* 4.6 0.9 - - - -
74B TRP* 3.5 38.8 - - + +
95B GLU* 4.0 9.2 - - - +
96B PRO* 1.3 78.3 - - - +
98B CYS* 1.3 64.0 + - - +
99B PHE* 3.8 15.3 - - + -
110B GLN* 3.8 35.2 - - + -
111B TRP 4.9 1.1 - - - +
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Residues in contact with CYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TRP* 3.7 28.5 - - + -
67B TRP* 3.6 16.8 - - + -
70B LEU 3.8 4.9 - - - -
71B SER* 3.8 6.7 - - - -
96B PRO* 4.9 0.4 - - - -
97B ILE* 1.3 78.2 - - - +
99B PHE* 1.3 66.8 + - - +
110B GLN* 3.2 7.8 - - - -
111B TRP 2.8 38.1 + - - +
113B CYS* 2.0 47.6 - - + -
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLN* 3.5 36.8 - - + -
94A VAL* 3.9 29.2 - - + -
25B TRP* 4.6 0.4 - - - +
67B TRP* 3.1 11.8 - - - -
68B ILE* 2.9 48.3 + - + +
70B LEU* 3.2 28.7 + - + +
72B HIS* 4.6 6.5 - + - -
97B ILE* 3.8 18.4 - - + -
98B CYS* 1.3 82.0 - - - +
100B VAL* 1.3 59.4 + - - +
108B TRP* 3.9 15.7 - - + -
109B ILE 3.4 15.3 - - - -
110B GLN* 3.8 24.0 - - + -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.6 9.9 - - + -
66B VAL 3.1 14.6 - - - +
67B TRP* 3.3 35.0 - - + -
68B ILE* 4.4 2.9 - - - -
99B PHE* 1.3 74.6 - - - +
101B ALA* 1.3 63.4 + - - +
107B LYS 3.8 0.2 - - - +
108B TRP* 3.3 5.2 - - - +
109B ILE* 2.9 48.8 + - + +
111B TRP* 3.6 33.0 - - + -
117B LYS* 4.2 16.4 - - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 4.2 7.2 - - + -
53B ILE* 6.2 0.4 - - + -
54B SER* 5.8 2.2 - - - +
64B VAL 3.2 0.7 - - - +
65B LEU* 3.2 9.0 - - - +
66B VAL* 2.7 47.1 + - + +
68B ILE* 3.7 16.2 - - + -
100B VAL* 1.3 75.1 - - - +
102B GLU* 1.3 63.0 + - - +
103B SER 4.0 0.2 - - - -
106B ASN* 5.3 2.5 - - - +
107B LYS 3.5 7.0 - - - +
108B TRP* 4.6 10.8 - - + +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER* 3.8 1.5 + - - -
64B VAL* 2.9 9.9 - - + +
65B LEU* 3.8 14.1 - - + -
101B ALA* 1.3 75.3 - - - +
103B SER* 1.3 57.6 + - - +
104B PHE* 2.9 35.2 + - - +
105B HIS* 2.6 47.2 + - - +
106B ASN* 2.9 35.0 + - - -
107B LYS* 3.1 31.6 + - + +
109B ILE* 4.6 9.4 - - + -
659C LEU* 4.6 12.5 - - + +
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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