Contacts of the strand formed by residues 19 - 25 (chain D) in PDB entry 4JRY
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 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.7 29.2 - - + -
12D SER 4.3 7.0 - - - -
13D MET* 3.0 49.4 - - + -
14D GLN* 3.0 24.2 + - - +
17D LYS* 3.5 45.8 - - + +
18D ASN* 1.3 83.1 + - - +
20D THR* 1.3 62.9 + - - +
89D LEU 3.8 0.2 - - - +
90D HIS* 3.3 3.8 - - - -
91D ILE* 2.7 39.4 + - + +
94D ALA* 4.6 0.2 - - + -
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Residues in contact with THR 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PRO* 4.8 3.1 - - - +
11D LEU* 4.5 5.2 - - - +
18D ASN* 4.4 5.0 + - - -
19D TYR* 1.3 75.0 - - - +
21D ILE* 1.3 69.0 + - - +
22D TYR* 3.4 40.2 + - + +
88D THR* 3.9 15.5 - - + -
89D LEU 3.2 7.2 - - - +
90D HIS* 3.1 38.3 + - + +
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Residues in contact with ILE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASN 3.8 6.7 - - - +
8D PRO* 4.1 4.3 - - + -
11D LEU* 3.8 20.4 - - + -
20D THR* 1.3 78.5 - - - +
22D TYR* 1.3 62.9 + - - +
41D TRP* 3.8 18.9 - - + -
88D THR* 3.4 6.2 - - - -
89D LEU* 2.9 69.3 + - + +
91D ILE* 4.4 9.9 - - + -
102D TYR* 3.9 17.5 - - + -
120D THR* 3.6 32.5 - - + +
122D LEU* 4.1 7.2 - - + -
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.2 8.1 + - - +
7D ASN* 2.8 71.0 + - - +
8D PRO* 5.0 2.0 - - + -
20D THR* 3.4 37.8 + - + +
21D ILE* 1.3 75.3 - - - +
23D CYS* 1.3 60.7 - - - +
24D ASN* 4.2 2.0 - - - +
41D TRP* 4.4 4.3 - - - -
86D LEU* 3.9 20.4 - - + -
87D SER 3.7 2.0 - - - -
88D THR* 3.6 27.6 - - + -
120D THR* 5.0 0.5 + - - -
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Residues in contact with CYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.7 19.1 - - - -
5D GLU 3.7 2.7 - - - -
6D GLN* 4.5 1.8 - - + -
22D TYR* 1.3 74.6 - - - +
24D ASN* 1.3 61.8 + - - +
25D TYR* 4.1 2.4 + - - -
39D LEU* 4.6 7.0 - - - -
41D TRP* 3.7 16.6 - - + -
85D ARG 4.0 0.3 - - - +
86D LEU* 3.4 6.4 - - - -
87D SER* 2.8 39.4 + - - +
104D CYS* 2.1 49.6 - - + -
106D VAL* 4.7 2.0 - - - -
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Residues in contact with ASN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.5 4.2 - - - +
5D GLU* 2.8 44.7 + - + +
7D ASN* 3.9 19.2 + - - -
22D TYR* 4.4 1.8 - - - +
23D CYS* 1.3 74.6 - - - +
25D TYR* 1.3 59.8 + - - +
84D ALA 4.3 5.0 - - - +
85D ARG 3.6 9.2 - - - +
86D LEU* 3.6 28.6 - - - +
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Residues in contact with TYR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LEU* 4.2 3.6 - - + -
3D LYS 3.2 12.3 - - - +
4D VAL* 4.1 5.4 - - + -
23D CYS 4.3 3.6 - - - -
24D ASN* 1.3 76.3 - - - +
26D SER* 1.3 58.1 + - - +
27D THR 2.9 28.9 - - - -
28D THR* 4.7 0.2 - - - -
29D SER* 3.6 28.0 + - - -
39D LEU* 3.7 31.6 - - + -
80D LEU* 3.8 10.6 - - + +
82D THR* 3.6 28.6 - - - +
85D ARG* 3.1 60.7 + - + +
86D LEU* 3.8 2.9 - - - -
106D VAL* 4.0 22.7 - - + -
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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