Contacts of the strand formed by residues 88 - 100 (chain D) in PDB entry 4R2G
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 ALA 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ARG* 3.9 12.6 - - - -
39D GLN 3.3 20.6 - - - +
40D SER* 3.3 13.2 - - - +
41D PRO* 4.1 4.0 - - - -
86D ASP 3.2 5.7 + - - +
87D THR* 1.3 77.1 - - - +
89D ILE* 1.3 63.4 + - - +
90D TYR* 3.2 24.1 - - + -
108D ALA* 4.8 0.4 - - - -
109D VAL 3.2 27.6 + - - -
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Residues in contact with ILE 89 (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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41C GLY* 4.5 24.9 - - - +
38D ARG* 3.1 3.8 - - - -
39D GLN* 2.9 56.4 + - + +
41D PRO* 6.1 1.8 - - + -
88D ALA* 1.3 74.3 - - - +
90D TYR* 1.3 62.7 + - - +
91D PHE* 3.7 28.9 - - + -
105D LYS 5.2 0.7 - - - +
106D GLY 4.2 4.0 - - - -
107D THR 3.3 24.5 - - - +
108D ALA* 4.4 14.6 - - + +
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Residues in contact with TYR 90 (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 GLU* 4.1 3.1 - - - +
18D LEU* 4.1 11.6 - - + +
20D VAL* 4.5 6.5 - - + -
36D TRP* 4.4 11.4 - - + -
37D ILE 4.1 2.2 - - - -
38D ARG* 3.2 33.5 + - + +
48D ILE* 3.9 9.2 - - + -
80D LEU* 3.5 31.4 - - + -
82D LEU* 3.7 17.0 - - + +
86D ASP* 2.5 30.9 + - - +
88D ALA* 3.2 24.5 - - + -
89D ILE* 1.3 72.2 - - - +
91D PHE* 1.3 60.3 + - - +
106D GLY* 3.3 1.9 - - - -
107D THR* 2.7 49.7 + - + +
109D VAL* 3.5 22.2 - - + -
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Residues in contact with PHE 91 (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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38C HIS* 4.3 5.4 - + - -
41C GLY 5.3 0.4 - - - -
42C GLN* 3.5 18.4 - - - -
43C ALA* 3.3 28.3 - - + -
44C PRO* 4.1 10.5 - - + -
6D GLU* 4.0 3.1 - - - +
36D TRP* 3.1 10.1 - - - -
37D ILE* 2.9 47.1 + - + +
38D ARG* 4.7 1.6 - - - -
39D GLN* 4.2 16.6 - - + -
45D LEU* 5.5 1.1 - - + -
89D ILE* 3.7 33.2 - - + -
90D TYR* 1.3 74.1 - - - +
92D CYS* 1.3 61.7 + - - +
103D TRP* 3.9 21.8 - + + -
104D GLY 3.7 17.3 - - - +
105D LYS 3.6 17.3 - - - -
106D GLY* 3.9 4.0 - - - -
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Residues in contact with CYS 92 (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 LEU* 3.8 9.7 - - - +
6D GLU* 3.0 19.0 + - - -
22D CYS* 2.0 48.5 - - + -
34D TRP* 5.8 0.7 - - - -
35D THR 3.3 8.5 - - - +
36D TRP* 3.5 26.4 - - + -
78D LEU* 4.5 7.0 - - + -
91D PHE* 1.3 76.0 - - - +
93D ALA* 1.3 64.2 + - - +
103D TRP* 4.0 0.2 - - - -
104D GLY 3.1 23.9 + - - -
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Residues in contact with ALA 93 (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 LEU* 4.0 2.2 - - - -
34D TRP* 3.6 12.9 - - - -
35D THR* 2.9 38.8 + - + +
37D ILE* 5.1 0.7 - - + -
92D CYS* 1.3 76.6 - - - +
94D THR* 1.3 61.3 + - - +
95D ALA 3.5 0.3 + - - -
100D MET* 4.0 20.4 - - + +
102D VAL 3.3 13.9 - - - +
103D TRP* 3.9 26.0 - - + -
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Residues in contact with THR 94 (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 VAL* 4.8 5.6 - - + +
4D LEU* 4.2 1.1 - - - +
32D TYR* 4.9 17.9 - - + -
33D TYR 4.0 8.7 - - - +
34D TRP* 3.6 19.0 - - + -
93D ALA* 1.3 69.4 - - - +
95D ALA* 1.3 62.0 + - - +
96D ARG* 3.7 19.7 - - + -
100D MET* 3.1 16.4 - - - -
101D ASP* 3.1 23.3 + - - +
102D VAL* 2.9 41.0 + - + +
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Residues in contact with ALA 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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32D TYR* 5.5 0.2 - - - +
33D TYR* 3.2 43.6 + - + +
34D TRP 4.8 0.4 - - - +
35D THR* 4.4 14.8 - - - +
47D TRP* 5.7 0.9 - - + -
50D TYR* 5.3 5.6 - - + -
93D ALA 3.5 3.4 + - - -
94D THR* 1.3 73.6 - - - +
96D ARG* 1.3 63.9 + - - +
100D TYR* 3.5 40.6 - - + +
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Residues in contact with ARG 96 (chain D).
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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32D TYR* 6.5 0.4 - - + -
33D TYR* 5.9 0.7 - - - -
94D THR* 3.7 17.0 - - + -
95D ALA* 1.3 79.4 - - - +
97D ARG* 1.3 60.3 + - - +
100D TYR* 2.9 73.9 + - + +
101D ASP* 3.2 31.4 + - - +
102D VAL* 5.7 0.2 - - - -
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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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33D TYR* 3.4 37.3 + - + -
54D ARG* 5.9 4.0 - - - +
95D ALA 4.2 0.8 + - - -
96D ARG* 1.3 68.7 - - - +
98D GLY* 1.3 64.0 + - - +
99D GLN* 5.5 0.4 - - - +
100D TYR* 3.3 97.1 + - + +
9R MAN 4.0 11.8 + - - -
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Residues in contact with GLY 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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96D ARG 3.6 4.6 + - - -
97D ARG* 1.3 76.1 - - - +
99D GLN* 1.3 60.0 + - - -
100D TYR* 2.9 69.9 + - - +
9R MAN 4.1 7.0 - - - -
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Residues in contact with GLN 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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97D ARG* 5.5 0.7 - - - +
98D GLY* 1.3 73.9 - - - -
100D TYR* 1.3 153.5 + - + +
7R MAN 6.2 0.2 - - - -
9R MAN 3.0 45.5 + - - +
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Residues in contact with ARG 100 (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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30C SER* 3.9 17.5 - - - -
31C ARG 3.6 8.1 + - - -
32C ALA* 3.7 16.2 - - + +
50C ASN* 5.8 1.1 - - - +
66C ASP* 3.1 31.7 - - - +
99D GLN* 1.3 69.8 - - - +
100D PHE* 1.3 167.5 + - - +
3R BMA 4.4 0.8 + - - -
4R MAN 3.4 27.2 + - - -
5R MAN 3.4 41.5 + - - +
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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