Contacts of the strand formed by residues 92 - 100 (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 ALA 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A PHE* 5.8 0.2 - - + -
86A LEU* 5.5 1.1 - - + -
88A VAL* 4.6 9.2 - - + -
90A GLU 3.5 3.6 + - - +
91A GLU* 1.3 78.2 - - - +
93A PHE* 1.3 69.9 + - - +
157A ARG* 3.6 3.8 - - - -
158A VAL* 2.9 42.1 + - + +
193A LEU* 4.2 14.4 - - + -
194A THR 3.3 14.1 - - - +
703A IYT 4.0 14.8 - - + +
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Residues in contact with PHE 93 (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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91A GLU* 3.5 30.5 - - + -
92A ALA* 1.3 81.7 - - - +
94A VAL* 1.3 62.6 + - - +
95A ILE* 3.6 2.5 + - + -
155A GLY* 4.9 1.1 - - - -
156A PHE 3.2 6.7 - - - +
157A ARG* 3.9 20.4 - - + -
193A LEU* 3.3 7.1 - - - -
194A THR* 2.7 44.6 + - + +
195A ARG 3.9 8.7 - - - -
196A VAL 3.4 15.9 - - - -
197A PRO* 3.6 26.7 - - + -
198A GLN* 3.8 26.5 - - + -
201A ILE* 3.8 30.7 - - + -
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Residues in contact with VAL 94 (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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93A PHE* 1.3 71.0 - - - +
95A ILE* 1.3 61.2 + - - +
96A ASP 3.9 11.7 - - - +
97A PHE* 3.5 35.0 - - + -
138A LEU* 5.3 1.8 - - + -
150A LEU* 3.9 6.0 - - - +
155A GLY* 3.2 4.7 - - - -
156A PHE* 2.8 38.3 + - + +
158A VAL* 4.0 17.7 - - + -
167A PHE* 3.9 21.3 - - + -
191A VAL* 4.2 8.1 - - + -
192A HIS 3.5 6.1 - - - +
193A LEU* 3.3 22.0 - - + -
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Residues in contact with ILE 95 (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 ASP* 4.3 2.7 - - - +
93A PHE 4.2 0.9 - - - +
94A VAL* 1.3 79.5 - - - +
96A ASP* 1.3 67.6 + - + +
149A ARG* 5.6 1.7 + - - +
150A LEU* 3.8 21.9 - - - +
154A VAL 4.0 9.2 - - - +
155A GLY* 4.1 0.4 - - - -
192A HIS* 2.9 46.6 + - + +
194A THR* 3.9 24.0 - - + -
198A GLN* 3.7 40.4 - - + +
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Residues in contact with ASP 96 (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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94A VAL* 3.7 5.9 - - - +
95A ILE* 1.3 81.9 - - + +
97A PHE* 1.3 87.7 + - - +
98A LYS* 3.6 15.4 + - - -
149A ARG* 2.8 57.4 + - - +
150A LEU* 4.4 3.4 + - - +
191A VAL* 3.5 3.8 - - - -
192A HIS* 3.0 42.2 + - + +
702A IYT 4.5 6.6 - - + +
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Residues in contact with PHE 97 (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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94A VAL* 3.5 25.8 - - + -
96A ASP* 1.3 87.5 + - - +
98A LYS* 1.3 68.2 + - - +
99A PRO* 4.2 4.3 - - - +
111A LEU* 3.9 11.4 - - + -
138A LEU* 3.8 25.4 - - + -
139A TYR* 3.5 51.6 + + + -
150A LEU* 4.1 19.5 - - + -
156A PHE* 4.0 8.5 - + - -
189A VAL* 4.2 3.1 - - + -
190A SER 3.3 6.7 - - - +
191A VAL* 3.5 22.7 - - + -
364A GOL 3.8 23.8 - - - -
702A IYT 4.4 0.2 - - - -
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Residues in contact with LYS 98 (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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96A ASP* 3.6 16.8 + - - +
97A PHE* 1.3 78.6 - - - +
99A PRO* 1.3 66.2 - - + +
100A ARG* 3.0 31.0 - - - +
149A ARG* 4.1 10.1 - - - +
189A VAL* 4.1 3.1 - - - -
190A SER 2.8 36.9 + - - -
702A IYT 3.3 69.0 + - + +
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Residues in contact with PRO 99 (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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97A PHE 4.2 2.7 - - - +
98A LYS* 1.3 86.8 - - + +
100A ARG* 1.3 70.1 + - - +
101A ALA* 3.7 2.2 - - + +
109A MET* 4.0 7.9 - - + -
139A TYR* 3.3 18.8 - - + +
141A TRP* 3.4 41.3 - - + +
147A PRO* 4.8 6.3 - - + -
188A GLY 3.9 4.9 - - - +
189A VAL* 4.4 3.4 - - + -
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Residues in contact with ARG 100 (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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46A GLU* 3.7 27.5 + - - +
65A ASP* 4.0 3.7 + - - -
67A ARG* 3.7 26.4 + - - +
98A LYS* 3.0 40.7 - - - +
99A PRO* 1.3 77.9 + - - +
101A ALA* 1.3 61.2 + - - +
186A CYS 4.5 0.3 - - - +
187A SER* 3.3 7.6 - - - -
188A GLY 2.8 33.2 + - - +
190A SER* 2.5 34.9 + - - +
702A IYT 3.5 23.6 + - - +
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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