Contacts of the strand formed by residues 145 - 151 (chain F) in PDB entry 3SDI
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 GLY 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141F VAL* 3.4 7.4 - - - -
142F ASP* 3.0 35.3 + - - +
143F LYS 3.9 0.2 - - - -
144F ASN* 1.3 76.9 - - - +
146F ALA* 1.3 63.2 + - - -
147F HIS* 3.4 3.9 + - - -
217F LEU* 6.5 1.3 - - - -
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Residues in contact with ALA 146 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F LYS* 4.0 20.1 - - + -
42F CYS 4.5 5.4 - - - +
43F ASN 5.6 0.4 - - - +
44F ASP* 4.0 6.1 - - - +
45F GLY* 3.3 48.7 - - - +
46F VAL* 4.2 2.2 - - + -
140F GLY 3.5 6.7 - - - +
141F VAL* 4.4 3.3 - - + +
145F GLY* 1.3 70.2 - - - -
147F HIS* 1.3 72.4 + - - +
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Residues in contact with HIS 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LYS* 4.6 3.4 - - - +
46F VAL* 3.3 8.7 - - - +
109F ILE* 3.8 20.1 - - + +
110F PRO* 3.8 24.5 - - + +
139F GLY* 3.1 23.2 - - - -
140F GLY 3.0 10.3 + - - -
142F ASP* 3.1 31.7 + - - -
144F ASN* 4.0 16.3 + - - -
145F GLY 3.4 10.6 + - - -
146F ALA* 1.3 80.0 + - - +
148F LEU* 1.3 59.5 + - - +
149F TYR* 3.7 22.7 - + + -
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY* 3.4 32.3 - - - +
40F ILE 4.0 3.1 - - - +
41F LYS* 4.0 17.7 - - + +
46F VAL* 4.3 6.5 - - + -
48F PHE* 3.7 31.2 - - + -
137F ILE* 3.7 18.6 - - + -
138F PHE 3.5 4.3 - - - +
147F HIS* 1.3 75.4 - - - +
149F TYR* 1.3 64.2 + - - +
159F GLY* 3.3 7.3 - - - -
160F TYR* 2.9 44.7 + - + +
161F LYS 4.1 0.7 - - - -
162F GLY* 3.8 23.1 - - - +
163F ALA* 4.0 4.5 - - + +
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Residues in contact with TYR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F ILE* 3.9 29.2 - - + -
110F PRO* 3.5 30.8 - - + +
113F ALA* 3.9 5.2 - - + -
136F THR 3.7 0.6 - - - +
137F ILE* 3.3 8.1 - - - +
138F PHE* 2.7 60.5 + + + -
147F HIS* 3.7 25.8 - + + -
148F LEU* 1.3 80.0 - - - +
150F MET* 1.3 59.9 - - - +
157F TYR* 3.8 27.4 - + + -
158F TRP 3.3 20.6 - - - -
159F GLY* 3.8 17.3 - - - -
160F TYR* 4.3 2.9 - - - -
163F ALA* 5.4 0.4 - - - -
63G THR* 4.4 14.2 - - + +
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Residues in contact with MET 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F SER* 4.7 2.5 - - - +
136F THR 3.3 9.9 - - - +
137F ILE* 3.8 21.5 - - + -
149F TYR* 1.3 75.5 - - - +
151F LEU* 1.3 65.9 + - - +
152F GLU* 3.4 32.2 - - - +
156F SER 3.7 0.5 - - - +
157F TYR* 3.0 25.4 - - - -
158F TRP 3.4 9.7 + - - -
160F TYR* 3.5 36.8 + - + +
163F ALA* 4.1 8.1 - - + -
164F ALA 3.5 26.9 - - - +
165F THR* 4.2 8.1 - - - -
173F LYS* 5.2 10.5 - - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F LEU* 4.1 13.5 - - + -
113F ALA 5.4 0.2 - - - +
116F LEU* 3.7 34.8 - - + -
117F GLY* 3.9 13.7 - - - -
120F VAL* 3.9 19.3 - - + -
134F VAL 4.2 0.9 - - - +
135F SER* 3.2 9.3 + - - -
136F THR* 3.0 35.7 + - - +
138F PHE* 4.0 10.3 - - + -
150F MET* 1.3 75.9 - - - +
152F GLU* 1.3 63.2 + - - +
155F GLY* 3.5 28.5 - - - +
156F SER 3.2 17.0 - - - +
157F TYR* 3.9 9.0 - - + -
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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