Contacts of the strand formed by residues 66 - 72 (chain A) in PDB entry 1X2W
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 6.3 0.2 - - + -
55A VAL* 3.9 32.1 - - + -
59A ILE* 4.1 18.8 - - + -
62A THR* 5.9 0.9 - - - +
64A SER 4.9 1.6 - - - +
65A TYR* 1.3 80.4 - - - +
67A TRP* 1.3 68.3 + - - +
68A ILE 3.6 0.3 + - - -
104A GLY* 2.9 6.3 - - - -
105A LEU* 2.7 50.1 + - + +
111A PHE* 4.1 14.1 - - + -
124A PRO* 3.6 13.7 - - + +
125A PHE* 3.9 21.5 - - - -
126A VAL* 4.5 3.4 - - + -
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Residues in contact with TRP 67 (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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21A LYS 2.8 20.6 + - - -
22A THR 3.6 3.8 - - - -
23A TRP* 3.4 26.2 - + + -
26A ALA* 3.6 20.6 - - + -
39A LEU* 4.0 14.5 - - + +
40A VAL* 3.8 11.6 - - - +
65A TYR 4.1 0.2 - - - -
66A VAL* 1.3 75.7 - - - +
68A ILE* 1.3 61.5 + - - +
102A CYS* 3.7 14.4 - - + -
103A LEU 3.6 11.9 - - - -
117A ILE* 3.2 29.4 - - + -
118A TYR 3.5 22.2 - - - -
119A CYS* 3.8 9.0 - - - -
121A GLN 3.4 21.3 - - - -
123A ASN* 3.5 27.7 + - - +
124A PRO 3.2 19.7 + - - -
125A PHE* 3.6 11.5 - - + +
126A VAL 4.1 10.9 + - - -
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Residues in contact with ILE 68 (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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23A TRP* 3.1 20.4 + - - -
39A LEU* 4.1 4.7 - - - -
40A VAL* 3.5 19.1 - - + +
42A ILE* 3.8 14.4 - - + -
66A VAL* 4.1 1.3 - - + +
67A TRP* 1.3 78.7 - - - +
69A GLY* 1.3 60.2 + - - +
70A LEU* 3.2 10.8 + - + +
103A LEU* 3.3 40.8 + - + +
105A LEU* 3.8 29.4 - - + -
114A TRP* 3.9 26.0 - - + +
79B TRP* 4.0 21.8 - - + -
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Residues in contact with GLY 69 (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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23A TRP* 3.8 12.6 - - - -
39A LEU* 3.8 20.2 - - - +
40A VAL 2.7 18.2 + - - -
68A ILE* 1.3 71.4 - - - +
70A LEU* 1.3 59.3 + - - +
71A ARG 3.6 0.7 + - - -
78B GLN 3.4 4.7 - - - +
79B TRP* 3.5 10.3 - - - -
80B SER* 3.1 30.1 + - - -
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Residues in contact with LEU 70 (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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68A ILE* 3.2 8.5 + - + +
69A GLY* 1.3 73.9 - - - +
71A ARG* 1.3 63.2 + - - +
103A LEU* 3.4 53.0 + - + +
114A TRP* 3.8 26.0 - - + -
77B TRP* 4.0 12.3 - - + -
78B GLN* 3.6 35.0 - - - +
79B TRP* 3.3 31.1 - - + +
85B LEU* 4.3 14.4 - - + -
90B TRP* 4.0 13.7 - - + -
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Residues in contact with ARG 71 (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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23A TRP* 3.2 60.7 - - + +
24A ASP* 3.4 4.8 + - - -
69A GLY 4.2 2.0 - - - +
70A LEU* 1.3 76.6 - - - +
72A VAL* 1.3 88.8 + - - +
73A GLN* 3.5 13.7 + - + +
74A GLY 3.3 9.9 + - - -
101A THR* 3.5 12.0 + - - +
102A CYS* 3.6 24.7 - - - -
119A CYS* 3.9 7.0 - - - +
404A SO4 2.7 43.2 + - - -
77B TRP* 3.4 14.6 - - - -
78B GLN 3.1 29.5 + - - +
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Residues in contact with VAL 72 (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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71A ARG* 1.3 104.9 + - - +
73A GLN* 1.3 55.2 + - - +
74A GLY 3.9 13.9 - - - +
76A GLU* 4.7 9.4 - - - +
101A THR* 3.1 38.3 + - + +
401A CL 4.2 3.4 - - + -
75B CYS* 3.7 27.1 - - + -
76B ASN 3.5 7.4 - - - -
77B TRP* 3.3 39.7 - - + -
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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