Contacts of the strand formed by residues 50 - 57 (chain A) 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 PHE 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 1.3 93.2 - - - +
51A GLY* 1.3 59.8 + - - +
99A GLY* 3.7 6.1 - - - +
100A LYS* 4.8 13.5 - - + -
101A ILE* 4.4 5.4 - - - +
117A ASN* 3.5 29.6 - - - -
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Residues in contact with GLY 51 (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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50A PHE* 1.3 76.5 - - - +
52A ASP* 1.3 69.2 + - - +
65A LEU* 5.9 2.2 - - - -
79A ILE* 5.5 3.1 - - - -
97A ILE 4.8 0.2 - - - -
98A SER* 3.3 4.3 - - - -
99A GLY 3.1 31.5 + - - -
101A ILE* 4.3 17.4 - - - +
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Residues in contact with ASP 52 (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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51A GLY* 1.3 77.5 - - - +
53A GLY* 1.3 60.8 + - - +
65A LEU* 4.7 10.4 - - - +
66A ARG 4.4 2.6 - - - +
67A SER* 5.6 1.2 - - - -
79A ILE* 4.9 10.0 - - - +
96A THR* 5.8 1.3 - - + -
97A ILE 3.5 9.6 - - - -
98A SER* 3.3 16.6 - - - +
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Residues in contact with GLY 53 (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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52A ASP* 1.3 81.2 + - - +
54A VAL* 1.3 65.8 + - - -
55A LEU 3.9 0.2 + - - -
65A LEU* 4.1 8.9 - - - +
66A ARG 3.2 14.8 - - - -
67A SER* 5.4 0.9 - - - -
68A ALA 6.0 0.4 - - - -
96A THR* 3.7 7.3 - - - +
97A ILE* 2.9 30.8 + - - +
98A SER* 4.5 0.4 + - - -
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Residues in contact with VAL 54 (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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53A GLY* 1.3 74.4 - - - -
55A LEU* 1.3 65.3 + - - +
56A GLU 3.7 0.2 + - - -
64A PHE 3.5 0.3 - - - +
65A LEU* 3.4 1.6 - - - -
66A ARG* 2.9 32.3 + - - +
68A ALA* 6.1 2.5 - - + -
72A TYR* 3.6 35.9 - - + +
94A GLY* 3.7 27.6 - - - +
95A ASP 4.0 2.9 - - - -
96A THR* 4.2 15.0 - - + +
245A MET* 3.7 20.8 - - + +
249A LYS* 4.4 17.9 - - + +
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Residues in contact with LEU 55 (chain A).
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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53A GLY 3.9 0.8 + - - -
54A VAL* 1.3 72.6 - - - +
56A GLU* 1.3 65.4 + - - +
57A ILE* 3.7 24.7 - - + -
63A GLY* 4.2 2.7 - - - -
64A PHE 3.5 16.8 - - - +
65A LEU* 3.7 9.6 - - + -
81A VAL* 3.7 30.1 - - + -
86A ILE* 4.9 3.6 - - + -
91A LEU* 3.7 33.9 - - + -
92A ARG 3.6 19.1 - - - +
93A THR* 3.7 1.8 - - - -
94A GLY 3.1 22.9 + - - -
95A ASP* 3.1 21.8 + - + +
97A ILE* 4.2 3.8 - - + -
245A MET* 3.4 9.7 - - - +
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Residues in contact with GLU 56 (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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55A LEU* 1.3 73.2 - - - +
57A ILE* 1.3 67.4 + - - +
58A LEU* 3.4 17.2 - - + +
63A GLY* 3.2 17.4 - - - -
64A PHE 2.8 18.0 + - - +
66A ARG* 2.4 52.0 + - + +
72A TYR 5.4 1.6 - - - +
93A THR* 4.3 5.6 - - + -
241A GLN* 2.8 43.3 + - - +
245A MET* 3.7 16.2 - - + +
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Residues in contact with ILE 57 (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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55A LEU* 3.7 21.7 - - + -
56A GLU* 1.3 73.9 - - - +
58A LEU* 1.3 77.2 + - - +
61A GLY* 3.9 14.4 - - - +
62A PHE 3.7 9.6 - - - +
63A GLY* 3.9 1.3 - - - -
86A ILE* 3.7 22.9 - - + -
91A LEU 3.4 27.4 - - - +
92A ARG* 3.7 15.5 - - - -
93A THR* 3.4 21.3 + - - +
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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