Contacts of the strand formed by residues 145 - 151 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141U VAL* 4.0 5.6 - - - -
142U ASP* 2.9 36.7 + - - +
143U GLU 3.7 1.0 + - - -
144U LEU* 1.3 75.3 - - - +
146U PRO* 1.3 79.8 - - - +
147U SER* 3.0 7.4 + - - -
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Residues in contact with PRO 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41U ARG* 3.4 39.1 + - + +
42U GLY 3.5 19.3 - - - +
43U LYS 3.7 15.3 - - - +
44U ASP* 4.1 2.0 - - - -
45U CYS 3.5 20.6 - - - +
46U THR* 3.4 17.7 - - - +
140U SER 3.5 3.6 - - - +
141U VAL* 4.1 10.0 - - + -
144U LEU 4.4 3.5 - - - +
145U GLY* 1.3 82.2 - - - +
147U SER* 1.3 60.1 + - - +
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Residues in contact with SER 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O MET* 6.1 1.3 - - - -
41U ARG* 4.2 2.4 - - - +
46U THR* 3.4 5.0 + - - +
109U CYS* 4.4 5.8 - - - -
110U ASP* 5.4 0.4 + - - -
138U PHE 4.3 0.7 - - - -
139U VAL* 3.3 6.9 - - - -
140U SER* 2.8 42.8 + - - +
142U ASP* 4.0 3.6 - - - +
144U LEU* 4.0 16.8 - - - +
145U GLY 3.0 15.9 + - - -
146U PRO* 1.3 71.7 + - - +
148U ILE* 1.3 67.4 + - - +
149U TYR* 3.8 23.8 + - - -
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Residues in contact with ILE 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O MET* 4.8 0.8 - - - +
39U ALA* 3.9 30.1 - - + +
40U VAL 3.9 2.9 - - - -
41U ARG* 3.4 26.0 - - + +
46U THR* 3.8 12.6 - - + -
137U THR* 3.6 26.5 - - + -
138U PHE 3.3 3.8 - - - +
139U VAL* 4.0 1.8 - - + -
147U SER* 1.3 79.2 - - - +
149U TYR* 1.3 69.3 + - - +
159U GLY* 3.2 5.4 - - - -
160U TYR* 3.0 44.5 + - + +
161U LYS 3.8 12.8 - - - +
162U ALA* 4.1 2.5 - - - -
163U THR* 3.9 17.0 - - + -
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Residues in contact with TYR 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O MET* 4.1 8.3 - - + +
63O THR* 3.9 22.5 - - - +
109U CYS* 3.9 19.5 - - - -
110U ASP* 3.5 33.2 - - + +
113U ALA* 3.6 21.1 - - + -
137U THR* 3.5 0.9 - - - -
138U PHE* 2.7 44.6 + - + +
144U LEU* 3.6 20.0 - - + +
147U SER* 3.8 23.0 + - - -
148U ILE* 1.3 79.3 - - - +
150U LYS* 1.3 60.5 + - - +
157U TYR* 4.2 14.1 - + + -
158U VAL 3.4 6.7 - - - +
159U GLY* 3.4 29.4 - - - -
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Residues in contact with LYS 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135U ILE* 3.6 20.6 - - + -
136U LEU 3.2 10.8 - - - +
137U THR* 3.9 13.7 - - + +
149U TYR* 1.3 75.3 - - - +
151U THR* 1.3 67.0 + - - +
156U TYR* 3.8 3.5 - - - +
157U TYR* 3.0 21.7 - - - +
158U VAL 3.1 10.6 + - - +
160U TYR* 3.5 31.4 + - + -
163U THR* 3.0 29.5 + - + +
164U ALA 3.0 21.6 + - - -
165U THR* 3.1 21.1 + - - +
169U GLN* 5.3 2.0 - - - +
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Residues in contact with THR 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113U ALA* 3.5 30.3 - - + +
116U MET* 4.7 1.0 - - + +
117U ALA* 4.3 13.6 + - - +
120U SER* 5.2 2.6 + - - -
134U VAL 4.2 0.5 - - - +
135U ILE* 3.2 8.6 - - - +
136U LEU* 2.9 55.6 + - - +
138U PHE* 4.0 17.5 - - + -
150U LYS* 1.3 78.3 - - - +
152U ASP* 1.3 63.5 + - - +
156U TYR 3.1 9.0 - - - -
157U TYR* 3.6 12.6 - - + -
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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