Contacts of the strand formed by residues 78 - 85 (chain A) in PDB entry 1SDW
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 THR 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 4.2 11.6 - - + +
74A LYS 4.7 1.0 + - - -
75A GLU* 2.7 36.9 + - - +
76A SER 4.0 0.2 + - - -
77A ASP* 1.3 78.1 - - - +
79A TYR* 1.3 61.5 + - - +
80A PHE* 3.6 45.5 - - + -
125A PHE* 4.2 14.5 - - + -
171A VAL 3.6 1.7 - - - +
172A HIS* 3.6 0.9 - - - -
173A TYR* 2.8 32.8 + - + +
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Residues in contact with TYR 79 (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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77A ASP* 3.7 12.1 - - + -
78A THR* 1.3 74.6 - - - +
80A PHE* 1.3 64.0 + - - +
108A HIS* 3.6 22.9 - + - -
125A PHE* 3.5 11.5 - - - +
126A CYS* 3.0 36.2 + - + +
127A ASP* 5.3 10.2 - - - +
170A GLN* 3.6 24.5 - - + -
171A VAL 3.5 3.4 - - - -
172A HIS* 3.5 43.1 + + + -
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Residues in contact with PHE 80 (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 MET* 3.1 22.6 - - + +
71A VAL* 3.4 34.1 - - + -
72A THR 4.2 9.6 - - - -
73A PRO* 4.1 19.5 - - + -
74A LYS* 6.3 1.1 - - - -
78A THR* 3.6 23.8 + - + -
79A TYR* 1.3 75.7 - - - +
81A CYS* 1.3 60.0 + - - +
123A TYR* 3.8 26.7 - + + -
124A TRP 3.5 11.9 - - - +
125A PHE* 3.7 27.4 - + - -
126A CYS* 3.3 5.4 - - - -
170A GLN* 3.4 2.8 - - - -
171A VAL 2.8 36.5 + - - +
173A TYR* 3.6 14.8 - + + -
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Residues in contact with CYS 81 (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 MET* 3.9 1.3 - - - -
80A PHE* 1.3 73.4 - - - +
82A MET* 1.3 61.4 + - - +
123A TYR* 3.1 8.5 - - - +
124A TRP* 2.8 63.0 + - + +
126A CYS* 2.0 45.5 - - - -
129A GLY 4.4 3.8 - - - -
130A THR* 4.5 7.9 - - - -
168A VAL* 4.7 6.7 - - + -
169A LEU 3.2 6.7 - - - +
170A GLN* 3.9 16.6 - - - -
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Residues in contact with MET 82 (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 ILE* 3.7 24.2 - - - -
67A ARG 3.0 26.7 - - - +
68A MET* 3.7 28.0 - - + -
69A PRO* 4.6 6.7 - - + -
81A CYS* 1.3 77.2 - - - +
83A SER* 1.3 77.2 + - - +
84A MET* 3.9 18.4 - - + -
122A SER 3.8 17.9 - - - +
123A TYR* 4.2 1.1 - - + -
124A TRP* 3.7 12.7 - - - -
168A VAL* 3.3 5.4 - - - +
169A LEU* 2.9 38.1 + - + -
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Residues in contact with SER 83 (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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82A MET* 1.3 82.3 - - - +
84A MET* 1.3 76.3 + - - +
117A PRO* 3.7 35.6 - - - +
119A SER 4.9 1.9 + - - -
121A GLY 5.3 3.4 + - - -
122A SER 5.0 2.1 + - - +
124A TRP* 3.9 7.8 - - - -
166A TYR* 4.2 8.4 - - - -
167A PHE 3.2 11.2 - - - -
168A VAL* 4.1 3.4 - - - -
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Residues in contact with MET 84 (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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48A LEU* 6.4 0.7 - - + -
53A PRO* 4.1 23.6 - - + -
64A LEU* 4.2 15.3 - - + -
65A ASP 3.9 19.5 - - - +
66A ILE* 3.7 32.8 - - + -
67A ARG 5.6 0.2 - - - -
82A MET* 3.9 14.6 - - + -
83A SER* 1.3 80.5 - - - +
85A ARG* 1.3 69.6 + - - +
86A LEU 3.7 0.3 + - - -
166A TYR* 4.0 2.9 - - - -
167A PHE* 2.9 39.9 + - + +
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Residues in contact with ARG 85 (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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64A LEU* 4.8 3.1 - - - +
84A MET* 1.3 83.1 - - - +
86A LEU* 1.3 79.0 + - - +
87A PRO* 3.5 5.5 - - - +
88A VAL 5.1 3.2 + - - -
89A ASP* 3.9 20.0 + - - -
165A LYS* 3.5 47.1 + - - +
166A TYR* 3.7 38.6 + - + -
167A PHE* 5.6 0.2 - - - -
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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