Contacts of the strand formed by residues 81 - 86 (chain A) in PDB entry 1UZX
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A THR* 3.5 4.9 - - - +
69A ILE* 2.9 39.8 + - + +
71A THR* 5.2 9.9 - - + -
80A SER* 1.3 83.4 - - - +
82A PRO* 1.3 70.0 - - + +
83A VAL* 3.6 24.2 + - + +
100A ILE* 5.4 5.6 - - + -
114A LEU* 6.1 2.5 - - + -
116A ILE* 4.0 42.0 - - + -
126A ILE* 4.4 3.1 - - + -
148A LEU* 4.2 17.7 - - + +
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Residues in contact with PRO 82 (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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67A GLY 3.6 8.3 - - - +
68A THR* 3.8 13.7 - - + +
80A SER 4.4 2.7 - - - +
81A ILE* 1.3 87.0 - - + +
83A VAL* 1.3 55.7 + - - +
100A ILE* 3.4 15.9 - - + +
101A ASN* 2.6 57.2 + - + +
105A PHE* 3.5 33.2 - - + -
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Residues in contact with VAL 83 (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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45A LEU* 5.0 3.6 - - + -
65A ILE 5.4 1.8 - - - +
66A TYR* 3.3 5.7 - - - +
67A GLY 2.9 41.5 + - - +
69A ILE* 3.7 26.9 - - + -
81A ILE* 3.8 29.2 - - + +
82A PRO* 1.3 81.0 - - - +
84A ILE* 1.3 67.4 + - - +
85A MSE 5.1 3.4 - - + +
98A ILE* 3.6 20.0 - - + -
99A SER 3.3 11.9 - - - +
100A ILE* 4.6 0.4 - - - -
101A ASN* 3.7 3.9 - - - +
126A ILE* 4.0 7.4 - - + -
148A LEU* 4.1 5.6 - - + -
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Residues in contact with ILE 84 (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 ARG* 3.9 12.8 - - - +
64A SER* 4.2 12.1 - - - +
65A ILE 3.7 4.0 - - - +
66A TYR* 4.3 2.5 - - + -
83A VAL* 1.3 77.3 - - - +
85A MSE 1.3 66.6 + - - +
86A TRP* 3.7 33.4 + - + +
97A PHE 3.9 0.3 - - - +
98A ILE* 3.3 4.5 - - - -
99A SER* 2.9 43.2 + - - +
100A ILE 5.3 0.4 - - - +
101A ASN* 3.8 35.0 - - + +
103A GLU* 3.9 11.7 - - + +
48B LYS* 6.2 4.5 - - + -
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Residues in contact with MSE 85 (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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38A LEU* 3.6 29.8 - - + -
64A SER* 3.1 7.6 - - - -
65A ILE* 2.8 50.4 + - + +
83A VAL* 4.1 2.9 - - + -
84A ILE* 1.3 74.1 - - - +
86A TRP* 1.3 71.0 + - - +
87A VAL* 4.4 5.2 - - + -
96A PRO* 4.0 11.9 - - + -
97A PHE 3.4 4.3 - - - +
98A ILE* 3.7 23.3 - - + +
141A LEU* 3.9 25.4 - - + +
144A VAL* 4.0 28.5 - - - -
145A VAL* 4.7 9.6 - - + -
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Residues in contact with TRP 86 (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 ARG* 3.8 41.1 - - + -
51A VAL 4.5 2.5 - - - -
52A PHE* 3.5 39.4 - + + -
62A LEU* 4.0 19.3 - - + -
63A LEU 4.0 1.3 - - - -
64A SER* 3.8 22.7 - - - -
84A ILE* 3.7 27.1 - - + +
85A MSE 1.3 76.8 - - - +
87A VAL* 1.3 60.8 + - - +
88A PRO* 3.7 1.1 - - - +
96A PRO* 3.2 24.6 - - - +
97A PHE* 2.8 43.4 + + + -
99A SER* 4.6 2.4 + - - -
125A TRP* 3.8 29.3 - + - -
46B ALA 4.7 5.1 + - - -
47B GLY* 5.3 4.3 - - - -
48B LYS* 5.9 4.3 - - + -
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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