Contacts of the strand formed by residues 90 - 99 (chain A) in PDB entry 3UAJ
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 TYR 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASN* 3.4 42.8 - - + +
84A GLU* 3.4 55.1 + - + +
85A GLU 5.4 0.9 - - - +
87A ASP* 3.3 34.9 + - - +
88A GLN 3.3 5.6 - - - +
89A GLN* 1.3 80.8 - - + +
91A ILE* 1.3 59.4 + - - +
92A CYS* 4.0 6.0 + - - -
116A CYS 4.1 2.2 - - - -
117A ALA 3.4 25.4 - - - -
118A LYS* 3.5 29.4 - - + +
234A LYS* 4.8 3.5 - - - +
1001A NAG 3.7 25.0 + - + +
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Residues in contact with ILE 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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65A ILE* 4.6 2.9 - - + -
89A GLN 4.3 0.6 + - - -
90A TYR* 1.3 70.2 - - - +
92A CYS* 1.3 64.1 - - - +
116A CYS* 3.4 2.6 - - - -
117A ALA* 2.9 48.3 + - + +
119A PHE* 4.8 7.0 - - + -
234A LYS* 3.7 24.7 - - + +
235A GLU* 3.6 38.8 - - + +
238A VAL* 3.9 29.4 - - + +
240A PHE* 3.5 29.5 - - + -
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Residues in contact with CYS 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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84A GLU 3.9 7.4 - - - -
85A GLU* 3.8 33.2 - - + +
90A TYR* 4.0 5.7 + - - -
91A ILE* 1.3 79.2 - - - +
93A ARG* 1.3 61.0 + - - +
94A ARG* 6.1 0.2 - - - -
114A VAL* 4.5 3.6 - - + -
115A THR 3.3 3.4 - - - -
116A CYS* 2.0 49.8 - - - -
240A PHE* 4.3 2.2 - - - -
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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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92A CYS* 1.3 74.7 - - - +
94A ARG* 1.3 72.4 + - - +
95A ASP* 3.3 30.5 + - - +
113A VAL 4.0 0.7 - - - +
114A VAL* 3.5 5.5 - - - +
115A THR* 3.3 27.8 + - - -
240A PHE* 3.8 60.5 + - + +
241A LYS 4.8 7.9 + - - -
242A VAL* 5.8 1.2 - - - +
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Residues in contact with ARG 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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79A GLU* 3.5 38.6 + - - +
80A PRO* 2.8 38.0 + - - +
81A TYR* 4.1 9.5 - - - +
85A GLU* 2.9 33.8 + - - +
92A CYS 6.1 0.2 - - - -
93A ARG* 1.3 80.0 + - - +
95A ASP* 1.3 66.0 + - - +
113A VAL 3.7 4.2 + - - +
114A VAL* 3.9 16.4 - - + +
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Residues in contact with ASP 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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93A ARG* 3.3 40.0 + - - +
94A ARG* 1.3 73.8 - - - +
96A VAL* 1.3 91.8 + - - +
97A VAL* 5.4 2.5 - - + +
112A GLY* 3.7 0.7 - - - -
113A VAL* 2.9 42.6 + - + +
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Residues in contact with VAL 96 (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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79A GLU* 5.8 2.7 - - - +
95A ASP* 1.3 96.9 + - - +
97A VAL* 1.3 64.6 + - - +
110A LYS* 4.1 39.7 - - + +
111A GLY 3.4 4.7 - - - +
112A GLY* 3.8 19.3 - - - +
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Residues in contact with VAL 97 (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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95A ASP* 5.4 2.9 - - + +
96A VAL* 1.3 76.7 - - - +
98A ASP* 1.3 61.3 + - - +
99A ARG* 3.2 23.5 + - - +
103A ASN* 5.5 1.3 - - - +
110A LYS* 3.4 4.2 - - - -
111A GLY 2.8 44.7 + - - +
113A VAL* 3.8 32.3 - - + +
242A VAL* 4.4 25.8 - - + +
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Residues in contact with ASP 98 (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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97A VAL* 1.3 70.3 - - - +
99A ARG* 1.3 58.9 + - - +
103A ASN* 3.1 24.1 + - - +
109A GLY 4.2 3.4 - - - -
110A LYS* 4.8 4.0 - - - +
5B GLY 3.6 18.1 - - - +
6B VAL* 4.7 4.2 - - - +
7B GLY* 3.3 29.0 + - - +
8B ASN 4.6 1.6 + - - -
316B GLN* 3.3 22.0 + - - +
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Residues in contact with ARG 99 (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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72A THR* 3.5 35.6 + - - +
73A ARG* 3.3 21.2 + - - +
74A CYS* 3.6 8.5 - - - +
75A PRO* 3.9 14.8 - - + -
97A VAL* 3.2 26.2 + - + +
98A ASP* 1.3 73.0 - - - +
100A GLY* 1.3 58.3 + - - +
103A ASN* 3.6 34.9 + - - +
104A GLY 4.7 1.8 + - - -
105A CYS* 3.3 26.3 - - - -
107A LEU 4.4 2.0 - - - -
108A PHE* 3.5 3.5 - - - +
109A GLY 2.9 38.9 + - - +
111A GLY* 3.8 13.0 - - - -
113A VAL* 4.4 6.9 - - - +
5B GLY* 4.6 6.2 + - - +
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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