Contacts of the strand formed by residues 94 - 99 (chain D) in PDB entry 2J3T
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 VAL 94 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D THR* 4.5 3.4 - - - -
32D PHE* 2.8 38.2 + - + +
66D ILE* 3.4 31.2 - - + -
67D ASN* 3.6 13.7 - - - +
85D TYR* 4.0 12.1 - - + -
86D LEU* 4.3 4.7 - - + -
91D ASN 3.8 8.1 - - - +
92D TYR* 3.4 32.1 - - + -
93D PRO* 1.3 76.2 - - - +
95D SER* 1.3 63.1 + - - +
96D ILE* 3.9 21.1 + - + -
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Residues in contact with SER 95 (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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29D GLU* 2.6 33.8 + - - +
30D LYS 3.6 5.8 - - - -
31D THR* 4.3 13.7 - - - +
65D ALA 3.8 0.2 - - - +
66D ILE* 3.1 5.2 - - - +
67D ASN* 2.5 52.2 + - - -
94D VAL* 1.3 72.3 - - - +
96D ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 96 (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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28D ALA 3.8 1.0 - - - +
29D GLU* 3.5 4.4 - - - -
30D LYS 3.0 31.0 + - - +
32D PHE* 3.9 23.6 - - + -
36D LEU* 4.0 20.6 - - + -
40D LEU* 5.3 0.9 - - + -
63D VAL* 3.7 28.9 - - + -
65D ALA 3.4 3.6 - - - +
66D ILE* 4.5 4.3 - - + -
86D LEU* 4.1 20.2 - - + -
94D VAL* 4.0 17.7 - - + -
95D SER* 1.3 79.4 + - - +
97D ARG* 1.3 62.1 + - - +
98D PHE* 3.6 34.1 - - + -
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Residues in contact with ARG 97 (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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27D GLU* 3.3 44.4 + - + +
28D ALA 3.2 15.7 - - - +
29D GLU* 2.9 31.8 + - + +
63D VAL* 3.6 2.6 - - - -
64D LEU* 2.6 38.3 + - + +
65D ALA* 2.8 27.3 + - + +
68D GLY* 4.3 21.0 + - - -
70D ASP* 3.4 24.7 + - - -
96D ILE* 1.3 72.5 - - - +
98D PHE* 1.3 57.5 + - - +
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Residues in contact with PHE 98 (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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27D GLU* 3.5 4.3 - - - +
28D ALA* 2.8 36.0 + - + +
30D LYS 5.6 0.2 - - - -
32D PHE* 3.7 21.1 - + - -
36D LEU* 6.4 0.2 - - + -
38D LEU* 3.9 14.8 - - + -
40D LEU* 4.1 9.0 - - + -
49D VAL* 3.7 28.7 - - + -
57D ILE* 3.2 35.2 - - + -
61D HIS* 3.8 17.1 + - + +
62D ALA 3.3 16.6 - - - +
63D VAL* 3.9 24.0 - - + -
64D LEU* 3.6 4.7 - - - -
96D ILE* 3.6 32.8 - - + -
97D ARG* 1.3 73.9 - - - +
99D GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 99 (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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27D GLU* 4.8 8.1 - - - -
61D HIS* 4.0 14.9 - - - +
62D ALA* 3.2 21.9 + - - +
64D LEU* 3.3 17.7 - - - +
98D PHE* 1.3 78.0 - - - +
100D ARG* 1.3 67.9 + - - -
101D PRO* 3.0 5.0 - - - +
102D ARG* 5.3 1.8 - - - -
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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