Contacts of the strand formed by residues 17 - 24 (chain A) in PDB entry 5J6Y
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 LEU 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PHE* 3.4 7.4 - - - -
16A GLY* 1.3 75.0 - - - -
18A VAL* 1.3 62.2 + - - +
19A GLY 3.3 0.5 + - - -
49A ALA* 2.9 36.4 + - + +
52A ILE* 3.8 21.8 - - + -
92A LEU* 3.9 23.1 - - + -
93A GLN 3.7 13.0 - - - +
94A GLY* 3.6 7.2 - - - -
95A TYR 3.5 39.7 - - - +
149A ILE* 3.8 20.4 - - + +
151A MET* 4.5 12.1 - - + -
182A LEU* 3.9 15.0 - - + -
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Residues in contact with VAL 18 (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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12A SER 5.6 0.9 - - - +
14A PHE* 4.0 13.0 - - + -
17A LEU* 1.3 70.3 - - - +
19A GLY* 1.3 64.9 + - - +
20A GLU* 5.1 9.3 - - + +
46A THR* 6.1 2.0 - - + -
47A PHE 4.3 1.1 - - - +
91A TYR 3.6 1.9 - - - +
92A LEU* 3.2 4.6 - - - -
93A GLN* 2.8 65.4 + - + +
184A SER* 4.1 25.8 - - - +
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Residues in contact with GLY 19 (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 3.3 2.6 + - - -
18A VAL* 1.3 75.1 - - - +
20A GLU* 1.3 64.0 + - - +
46A THR* 3.2 9.9 - - - -
47A PHE* 2.8 52.4 + - - +
91A TYR 3.6 3.8 - - - -
92A LEU* 3.7 15.9 - - - -
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Residues in contact with GLU 20 (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 VAL* 5.1 10.2 - - + +
19A GLY* 1.3 78.8 - - - +
21A TYR* 1.3 60.7 + - - +
22A TYR* 2.7 39.9 + - + -
38A VAL* 4.6 0.5 - - - +
43A ALA* 3.8 14.6 + - + +
45A ALA 3.5 4.0 - - - -
46A THR* 4.4 8.8 - - + +
47A PHE* 3.8 3.7 - - - -
90A ILE* 3.2 6.1 - - - +
91A TYR* 2.9 58.4 + - + +
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Residues in contact with TYR 21 (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 GLU* 1.3 73.5 - - - +
22A TYR* 1.3 68.6 + - - +
23A GLY* 3.7 18.5 - - - -
43A ALA 3.7 0.9 - - - -
44A ASP* 2.8 37.3 + - + -
45A ALA* 2.8 19.7 + - + +
47A PHE* 4.2 11.2 - - + -
61A VAL* 4.6 7.4 - - + -
62A ALA* 3.1 36.6 + - - +
67A LEU* 3.6 38.1 - - + -
82A PRO* 3.7 37.9 - - + +
85A ASN* 4.8 3.0 + - - +
88A GLY* 4.0 2.8 - - - -
89A GLY* 3.2 29.4 - - - -
90A ILE* 4.3 2.9 - - + +
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Residues in contact with TYR 22 (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 GLU* 2.7 46.4 + - + -
21A TYR* 1.3 82.5 - - - +
23A GLY* 1.3 59.5 + - - +
34A PHE* 4.2 8.3 - + + -
37A LEU* 3.7 26.0 - - + +
38A VAL* 3.6 41.8 + - + +
41A LYS* 3.3 33.9 - - - -
42A GLU 3.7 0.9 - - - -
43A ALA* 3.5 23.2 + - + -
44A ASP* 3.6 3.1 - - - -
88A GLY* 3.1 2.1 - - - -
89A GLY 2.9 33.3 + - - -
91A TYR* 4.7 2.2 - - + -
306A CA 2.6 20.4 - - - -
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Residues in contact with GLY 23 (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 TYR* 3.7 12.4 - - - -
22A TYR* 1.3 74.5 - - - +
24A THR* 1.3 65.0 + - - -
37A LEU* 3.8 1.7 - - - +
41A LYS* 2.8 27.5 + - - -
44A ASP* 2.8 10.5 + - - -
85A ASN* 3.5 20.7 + - - +
87A ASP 3.4 9.6 - - - -
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Residues in contact with THR 24 (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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23A GLY* 1.3 74.4 - - - -
25A ASN* 1.3 63.5 + - - +
26A SER* 2.8 40.8 + - - +
28A LEU* 4.1 10.3 - - + -
37A LEU* 3.8 31.4 - - + +
41A LYS* 5.1 0.2 - - - +
85A ASN* 3.4 12.3 - - - -
86A THR* 3.2 5.4 + - - -
87A ASP* 2.9 43.4 + - + +
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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