Contacts of the strand formed by residues 49 - 57 (chain D) in PDB entry 6XAV
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 ILE 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 4.1 11.4 - - - +
3D LEU* 4.7 0.9 - - + -
39D LEU* 3.4 61.7 - - + +
42D HIS* 4.8 7.9 - - - +
43D ALA* 3.7 19.5 - - + +
47D GLU 4.5 1.1 - - - +
48D ASP* 1.3 79.3 - - - +
50D PHE* 1.3 65.9 + - - +
100D LYS* 3.6 5.4 - - - +
101D ILE* 2.8 60.2 + - + +
102D ARG 5.4 0.2 - - - -
103D PRO* 3.8 18.4 - - + -
111D PHE* 5.6 1.1 - - + -
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Residues in contact with PHE 50 (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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1D MET 3.0 35.3 + - - +
2D ASN* 3.3 13.2 - - + +
3D LEU* 3.5 6.6 + - - +
48D ASP* 4.0 25.6 - - + -
49D ILE* 1.3 75.5 - - - +
51D GLY* 1.3 58.5 + - - +
99D GLY 3.7 8.5 - - - +
100D LYS* 3.7 47.3 - - + -
101D ILE* 3.9 5.5 - - - +
117D ASN* 4.2 13.9 - - - -
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Residues in contact with GLY 51 (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 ASN* 3.6 11.2 - - - -
3D LEU* 4.0 8.7 - - - -
50D PHE* 1.3 76.4 - - - +
52D ASP* 1.3 66.9 + - - +
65D LEU* 5.5 0.4 - - - +
79D ILE* 3.7 19.6 - - - +
98D SER* 3.7 1.6 - - - -
99D GLY 3.2 28.4 + - - +
101D ILE* 3.9 3.0 - - - +
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Residues in contact with ASP 52 (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 ASN* 2.6 39.4 + - - +
3D LEU* 4.9 5.1 - - - +
4D THR* 3.3 28.1 + - - +
51D GLY* 1.3 72.7 - - - +
53D GLY* 1.3 63.1 + - - +
65D LEU* 4.3 6.3 - - - +
66D ARG 4.6 0.5 - - - +
67D SER* 5.9 0.7 - - - -
79D ILE* 3.5 16.2 - - - +
96D THR* 5.5 3.4 - - + +
97D ILE 3.3 8.3 - - - -
98D SER* 3.2 25.1 - - - +
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Residues in contact with GLY 53 (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 THR* 6.1 0.2 - - - -
52D ASP* 1.3 83.9 + - - +
54D VAL* 1.3 67.6 + - - -
65D LEU* 3.5 12.7 - - - +
66D ARG 3.2 14.1 - - - -
67D SER* 5.4 0.9 - - - -
96D THR* 4.5 6.0 - - - +
97D ILE 3.0 28.5 + - - +
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Residues in contact with VAL 54 (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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53D GLY* 1.3 73.2 - - - -
55D LEU* 1.3 64.8 + - - +
56D GLU 3.6 0.3 + - - -
64D PHE 3.3 0.7 - - - +
65D LEU* 4.0 1.1 - - - -
66D ARG* 2.9 30.7 + - - +
68D ALA* 5.9 2.2 - - + +
72D TYR* 3.6 34.8 - - + +
94D GLY* 3.7 32.1 - - - +
95D ASP 4.0 3.6 - - - -
96D THR* 4.0 17.3 - - + +
245D MET* 3.7 17.2 - - + +
249D LYS* 4.4 18.8 - - + +
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Residues in contact with LEU 55 (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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53D GLY 3.7 1.0 + - - -
54D VAL* 1.3 72.8 - - - +
56D GLU* 1.3 64.8 + - - +
57D ILE* 3.7 22.0 - - + -
63D GLY* 3.9 9.0 - - - -
64D PHE 3.3 18.4 - - - +
65D LEU* 3.7 6.5 - - + -
81D VAL* 3.7 31.9 - - + -
86D ILE* 4.9 1.8 - - + -
91D LEU* 3.7 32.5 - - + -
92D ARG 3.5 20.9 - - - +
93D THR* 3.6 2.6 - - - -
94D GLY 3.2 19.9 + - - -
95D ASP* 3.2 20.9 + - + +
97D ILE* 4.6 2.2 - - + -
245D MET* 3.4 9.8 - - - +
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Residues in contact with GLU 56 (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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55D LEU* 1.3 73.3 - - - +
57D ILE* 1.3 66.0 + - - +
58D LEU* 3.3 21.5 - - + +
63D GLY* 3.2 16.4 - - - -
64D PHE* 2.8 17.7 + - + +
66D ARG* 3.2 35.7 + - + +
72D TYR 3.8 9.8 - - - +
74D ALA* 6.0 1.7 - - - +
93D THR* 4.4 2.5 - - + -
241D GLN* 2.8 44.6 + - - +
245D MET* 3.6 21.0 - - + +
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Residues in contact with ILE 57 (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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55D LEU* 3.7 24.2 - - + -
56D GLU* 1.3 73.9 - - - +
58D LEU* 1.3 77.4 + - - +
61D GLY* 3.6 20.6 - - - +
62D PHE 3.7 4.3 - - - +
63D GLY* 3.8 1.3 - - - -
86D ILE* 4.1 15.9 - - + -
91D LEU 3.4 25.4 - - - +
92D ARG* 3.8 16.2 - - + -
93D THR* 3.5 20.9 + - - +
241D GLN* 5.8 0.5 + - - -
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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