Contacts of the strand formed by residues 83 - 91 (chain A) in PDB entry 4Y22
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 SER 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU* 3.7 2.8 - - - +
23A VAL* 2.7 34.5 + - - +
80A GLN* 2.4 39.2 + - - +
81A PRO 4.9 0.2 - - - -
82A GLY* 1.3 79.5 - - - +
84A VAL* 1.3 67.8 + - - +
85A ALA* 5.3 1.7 - - - +
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Residues in contact with VAL 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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20A ARG* 3.8 35.7 - - + +
21A GLY 3.4 11.7 - - - +
22A GLU* 4.2 21.1 - - + +
83A SER* 1.3 80.3 + - - +
85A ALA* 1.3 64.0 + - - +
101A PRO* 5.2 3.5 - - - +
129A LYS* 6.3 0.7 - - + -
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Residues in contact with ALA 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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20A ARG* 3.5 2.4 - - - +
21A GLY 3.1 30.9 + - - +
23A VAL* 4.2 13.2 - - + -
79A PHE* 3.5 37.0 - - + -
83A SER* 4.0 2.8 + - - +
84A VAL* 1.3 78.6 - - - +
86A GLU* 1.3 59.8 + - - +
101A PRO* 4.2 10.8 - - + -
126A PHE* 3.8 10.8 - - + -
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Residues in contact with GLU 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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18A ARG* 3.9 26.6 + - - +
19A VAL 3.3 17.3 - - - +
20A ARG* 4.1 19.3 + - + +
85A ALA* 1.3 76.6 - - - +
87A VAL* 1.3 66.9 + - - +
88A CSO 4.1 25.6 - - - +
99A LYS 3.9 2.1 - - - +
100A LEU 4.1 0.3 - - - -
101A PRO* 3.4 34.3 - - + +
130A CSO 4.2 9.2 + - - -
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Residues in contact with VAL 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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17A LEU 3.2 6.1 - - - +
18A ARG* 3.5 0.3 - - - -
19A VAL* 3.0 41.7 + - + +
30A PHE* 5.8 2.5 - - + -
32A LEU* 3.6 29.4 - - + -
45A PHE* 4.2 12.6 - - + -
79A PHE* 4.1 17.0 - - + -
85A ALA 5.8 0.2 - - - -
86A GLU* 1.3 78.6 - - - +
88A CSO 1.3 61.8 + - - +
89A ILE* 4.0 12.9 - - + +
98A VAL* 5.0 1.8 - - + -
99A LYS 3.5 2.9 - - - +
100A LEU* 3.8 25.4 - - + -
126A PHE* 5.4 6.5 - - + -
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Residues in contact with CSO 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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16A CYS* 3.6 18.4 - - - -
17A LEU 3.5 3.1 - - - -
18A ARG* 3.7 31.8 + - - -
86A GLU* 4.1 20.5 - - - +
87A VAL* 1.3 76.1 - - - +
89A ILE* 1.3 62.0 + - - +
97A THR 3.5 2.9 - - - +
98A VAL* 3.7 0.5 - - - -
99A LYS* 2.8 64.0 + - + +
100A LEU 6.1 0.7 - - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.2 3.3 - - + +
15A GLU 3.7 2.6 - - - +
16A CYS* 4.6 1.1 - - - -
17A LEU* 2.8 51.9 + - + +
19A VAL* 5.1 1.1 - - + -
32A LEU* 4.4 13.5 - - + -
34A LEU* 3.7 35.0 - - + -
43A LEU* 4.4 12.8 - - + -
45A PHE* 6.1 3.6 - - + -
87A VAL* 4.3 22.9 - - + -
88A CSO 1.3 79.2 - - - +
90A THR* 1.3 70.0 + - - +
96A LEU* 4.2 13.7 - - + -
97A THR 3.3 8.7 - - - +
98A VAL* 4.5 17.7 - - + -
117A ILE* 5.4 1.8 - - + -
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Residues in contact with THR 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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11A LEU* 5.3 0.7 - - - -
14A GLY* 3.5 22.0 - - - -
15A GLU 3.4 21.2 + - - -
16A CYS* 4.5 6.7 - - - -
89A ILE* 1.3 77.5 - - - +
91A PHE* 1.3 71.1 + - - +
96A LEU* 3.6 4.0 - - - +
97A THR* 2.7 51.5 + - + +
99A LYS* 3.8 16.4 - - - +
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Residues in contact with PHE 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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11A LEU* 3.4 32.1 - - + -
12A LYS 3.9 10.5 - - - -
13A PRO* 3.1 32.6 - - + +
14A GLY* 3.0 25.3 + - - -
42A CYS* 6.3 0.2 - - - -
90A THR* 1.3 88.1 + - - +
92A ASP* 1.3 81.3 + - - +
93A GLN* 5.9 0.2 - - + -
95A ASN 3.3 13.7 - - - +
96A LEU* 3.6 17.7 - - + -
97A THR* 4.5 1.8 - - - +
110A ASN* 3.9 11.0 - - - -
114A LEU* 3.8 19.3 - - + -
116A ALA* 4.1 11.4 - - - -
117A ILE* 3.8 27.4 - - + -
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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