Contacts of the strand formed by residues 166 - 173 (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 TYR 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A SER* 4.2 8.3 - - - -
84A MET 3.5 6.7 - - - -
85A ARG* 3.7 52.4 + - + -
86A LEU* 4.6 1.1 - - - +
113A GLY* 3.3 5.4 - - - -
114A CYS* 2.8 36.0 + - - +
115A ASN 3.7 24.9 - - - -
117A PRO* 3.5 37.0 - - + -
164A SER* 3.8 4.1 - - - -
165A LYS* 1.3 89.1 - - + +
167A PHE* 1.3 69.6 + - - +
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Residues in contact with PHE 167 (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* 3.8 19.5 - - + -
66A ILE* 3.7 27.5 - - + +
83A SER* 3.2 5.9 - - - -
84A MET* 2.9 41.6 + - + +
86A LEU* 3.4 33.7 - - + -
94A VAL* 3.9 25.4 - - + -
111A LEU* 4.2 17.3 - - + -
112A PHE 3.2 4.7 - - - +
113A GLY* 4.8 0.9 - - - -
138A LEU* 3.6 32.1 - - + -
158A VAL* 4.6 9.4 - - + -
164A SER* 6.2 0.7 - - - -
166A TYR* 1.3 78.8 - - - +
168A VAL* 1.3 62.3 + - - +
191A VAL* 4.2 12.3 - - + -
193A LEU* 4.5 1.8 - - + -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A CYS* 4.7 4.3 - - - -
82A MET 3.3 11.0 - - - +
83A SER* 4.1 2.9 - - - -
111A LEU* 3.5 3.2 - - - -
112A PHE* 2.8 41.0 + - + +
114A CYS* 3.7 9.4 - - - -
117A PRO* 4.0 18.8 - - + -
124A TRP* 4.1 11.7 - - + -
130A THR* 3.6 33.2 - - + +
131A CYS* 3.5 25.4 - - - -
166A TYR* 4.8 0.2 - - + -
167A PHE* 1.3 79.7 - - - +
169A LEU* 1.3 68.2 + - - +
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Residues in contact with LEU 169 (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* 3.5 41.5 - - + +
68A MET* 3.7 4.4 - - + +
80A PHE 3.7 1.0 - - - +
81A CYS* 3.2 7.3 - - - +
82A MET* 2.9 45.4 + - + -
109A MET* 4.4 5.6 - - + -
110A LEU 3.5 15.7 - - - +
111A LEU* 4.1 9.0 - - + -
167A PHE 4.2 0.6 - - - -
168A VAL* 1.3 74.8 - - - +
170A GLN* 1.3 66.1 + - - +
171A VAL* 3.7 23.8 - - + -
187A SER 3.9 4.7 - - - +
188A GLY* 3.8 9.4 - - - -
189A VAL* 4.3 23.6 - - + +
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Residues in contact with GLN 170 (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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79A TYR* 3.6 24.0 - - + -
80A PHE 3.4 4.3 - - - -
81A CYS* 3.9 7.6 - - - -
108A HIS* 2.9 28.8 + - - +
109A MET* 3.1 6.2 - - - +
110A LEU* 2.9 47.2 + - + +
112A PHE* 4.2 12.4 - - + -
126A CYS* 3.7 24.9 - - - +
130A THR* 4.4 11.1 + - - -
168A VAL 4.1 0.4 + - - -
169A LEU* 1.3 73.9 - - - +
171A VAL* 1.3 65.7 + - - +
701A IYT 3.8 22.5 - - - +
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Residues in contact with VAL 171 (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* 3.6 29.2 - - + -
78A THR 3.6 1.4 - - - +
79A TYR* 3.5 1.0 - - - -
80A PHE 2.8 34.0 + - - -
106A VAL* 4.0 26.9 - - + -
108A HIS 3.7 2.2 - - - -
109A MET* 4.1 11.4 - - + -
169A LEU* 3.7 22.2 - - + -
170A GLN* 1.3 80.8 - - - +
172A HIS* 1.3 62.9 + - - +
173A TYR* 3.6 33.2 + - + +
187A SER* 4.3 4.9 - - - +
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Residues in contact with HIS 172 (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* 3.3 31.4 + - - -
78A THR 3.6 5.4 - - - -
79A TYR* 3.5 43.1 - + + +
106A VAL* 3.5 4.5 - - - +
107A HIS* 2.7 48.5 + + + -
108A HIS* 2.8 38.3 + - + +
170A GLN* 4.2 0.8 - - - +
171A VAL* 1.3 71.6 - - - +
173A TYR* 1.3 66.7 + - - +
357A CU 2.1 28.6 - - - -
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Residues in contact with TYR 173 (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* 3.7 18.8 - - + +
71A VAL* 3.7 9.6 - - + +
73A PRO* 3.5 31.6 - - + -
76A SER* 4.4 0.2 - - - -
77A ASP* 2.8 29.8 + - - -
78A THR 2.8 24.5 + - - +
80A PHE* 3.6 26.7 - + + -
105A THR* 3.5 27.6 - - + +
106A VAL* 4.0 14.6 - - + -
171A VAL* 3.6 25.1 - - + +
172A HIS* 1.3 72.5 - - - +
174A GLY* 1.3 61.3 + - - +
176A ILE* 4.6 2.7 - - + -
179A PHE* 4.2 3.1 - + - -
185A ASP* 2.5 41.2 + - + -
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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