Contacts of the strand formed by residues 60 - 67 (chain A) in PDB entry 1CXQ
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LEU* 2.9 39.5 + - + +
59A GLN* 1.4 77.3 - - - +
61A TRP* 1.3 75.1 + - - +
62A GLN* 5.7 0.2 - - + -
82A ASP* 3.8 1.7 + - - +
83A THR* 2.7 46.3 + - + +
116A LYS* 5.5 0.7 - - + -
117A ALA* 3.3 24.7 - - + +
119A LYS* 4.9 9.2 - - + +
302A GOL 5.0 7.9 - - - +
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Residues in contact with TRP 61 (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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59A GLN* 5.0 0.8 - - - +
60A ILE* 1.3 84.4 - - - +
62A GLN* 1.3 58.8 + - - +
80A THR* 3.6 20.0 - - + -
81A VAL 3.3 7.2 - - - +
82A ASP* 3.8 23.7 + - - +
83A THR* 4.4 0.2 - - - -
105A TRP* 3.9 16.8 - + - -
108A ALA* 3.6 34.8 - - + -
109A ILE* 3.7 9.6 - - + -
112A LEU* 3.7 27.8 + - + +
113A GLY 3.2 24.2 - - - -
115A PRO* 3.5 35.4 - - + +
117A ALA 3.0 9.9 + - - +
118A ILE* 3.4 24.8 - - + -
119A LYS* 2.8 33.7 + - - +
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Residues in contact with GLN 62 (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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60A ILE* 5.7 0.9 - - + -
61A TRP* 1.3 77.0 - - - +
63A THR* 1.3 63.1 + - - +
80A THR* 3.3 2.3 - - - -
81A VAL* 2.9 36.0 + - + +
83A THR* 3.8 18.6 - - + +
119A LYS* 3.3 16.5 - - + +
152A GLY 3.8 7.3 + - - -
153A GLN* 3.1 34.9 - - + +
154A ALA 4.6 0.2 - - - +
155A MET* 3.3 18.5 + - - +
156A VAL* 2.9 40.9 + - + +
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Residues in contact with THR 63 (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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61A TRP* 4.6 0.2 - - - +
62A GLN* 1.3 74.8 - - - +
64A ASP* 1.3 70.1 + - - +
65A PHE* 5.9 0.9 - - + -
78A ALA* 5.5 1.3 - - + -
79A VAL 3.2 10.8 - - - +
80A THR* 2.7 23.4 + - - +
101A ALA* 6.1 0.7 - - + -
104A HIS* 4.0 11.9 - - + -
105A TRP* 2.9 41.0 + - + +
118A ILE* 3.6 6.5 - - - +
119A LYS 3.0 13.9 + - - +
120A THR* 3.8 19.7 - - - +
126A PHE* 4.1 13.2 - - + -
153A GLN* 4.1 4.9 + - - -
156A VAL* 4.2 2.5 - - - -
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Residues in contact with ASP 64 (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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63A THR* 1.3 77.1 - - - +
65A PHE* 1.3 82.0 + - - +
77A LEU 3.8 0.2 - - - +
78A ALA* 3.6 2.9 - - - -
79A VAL* 2.9 33.4 + - - +
121A ASP* 4.0 18.0 - - - +
126A PHE* 4.2 8.8 - - - -
153A GLN* 4.2 13.3 + - - +
156A VAL* 3.9 21.9 - - + +
157A GLU* 4.9 5.5 - - - +
160A ASN* 3.1 23.4 + - - +
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Residues in contact with PHE 65 (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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63A THR* 5.9 1.1 - - + -
64A ASP* 1.3 93.2 + - - +
66A THR* 1.3 61.5 + - - +
76A TRP* 3.8 27.6 - + + -
77A LEU 3.2 14.6 - - - -
78A ALA* 3.7 21.8 - - + -
93A HIS* 4.3 8.5 - + + -
96A VAL* 3.8 22.0 - - + -
97A THR 4.2 2.7 - - - -
100A ALA* 4.1 15.3 - - + -
101A ALA* 3.7 33.9 - - + -
125A CYS* 3.6 26.9 - - - -
126A PHE* 3.7 21.0 - + - -
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Residues in contact with THR 66 (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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65A PHE* 1.3 77.1 - - - +
67A LEU* 1.3 60.5 + - - +
68A GLU 3.7 0.2 + - - -
76A TRP* 3.6 4.7 - - - -
77A LEU* 2.8 52.2 + - + +
79A VAL* 4.2 5.2 - - + -
160A ASN* 3.9 34.6 + - + +
163A LEU* 5.3 0.9 - - + -
164A LYS* 2.9 43.3 + - + -
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Residues in contact with LEU 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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66A THR* 1.3 73.8 + - - +
68A GLU* 1.3 59.3 + - - +
69A PRO* 3.7 19.0 - - + +
75A SER* 3.6 34.3 - - - +
76A TRP* 3.5 43.4 - - + +
164A LYS* 4.1 13.9 + - - +
300A EPE 5.0 6.5 - - - -
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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