Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 1SMN
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 SER 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A THR* 3.9 14.7 - - - +
48A LYS* 4.2 13.1 - - - +
134A ILE* 3.6 9.5 - - - +
138A ASP 3.8 2.9 + - - -
139A ILE* 1.3 74.6 - - - +
141A SER* 1.3 68.0 + - - +
177A ASN* 2.9 18.3 + - - -
178A ASN* 5.8 1.0 + - - -
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Residues in contact with SER 141 (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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45A HIS* 2.7 29.8 + - - -
46A ILE 3.3 6.7 - - - -
47A THR* 4.3 1.4 - - - +
134A ILE* 3.7 1.8 - - - +
139A ILE* 3.6 5.3 - - - +
140A SER* 1.3 85.5 + - - +
142A VAL* 1.3 67.3 + - - +
143A TYR* 3.7 17.8 + - - -
176A ILE* 3.4 4.0 - - - -
177A ASN* 2.9 34.0 + - - -
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Residues in contact with VAL 142 (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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44A TYR 3.8 0.5 - - - +
45A HIS* 3.3 5.0 - - - -
46A ILE* 2.8 46.7 + - + +
130A GLU* 4.0 19.3 - - + +
133A LEU* 3.9 31.4 - - + -
134A ILE* 4.1 15.5 - - + +
139A ILE* 4.3 3.6 - - + -
141A SER* 1.3 79.9 - - - +
143A TYR* 1.3 62.6 + - - +
144A THR* 3.7 9.8 + - - +
174A ILE* 3.5 28.9 - - + -
175A PHE 3.7 4.3 - - - +
176A ILE* 4.4 1.8 - - + -
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Residues in contact with TYR 143 (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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7A ASP 4.3 5.4 + - - -
8A ASN 3.6 21.8 - - - +
9A CYS 4.0 3.1 - - - +
10A ALA* 3.6 31.9 - - + +
44A TYR 3.5 1.6 - - - -
45A HIS* 3.3 43.2 + + + -
141A SER* 3.7 13.8 + - - -
142A VAL* 1.3 73.0 - - - +
144A THR* 1.3 63.0 + - - +
145A VAL* 5.9 0.2 - - - -
173A VAL 4.0 0.5 - - - +
174A ILE* 3.5 1.9 - - - -
175A PHE* 2.9 73.9 + + + -
177A ASN 3.5 22.0 - - - -
219A TRP* 5.6 0.2 + - - -
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Residues in contact with THR 144 (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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8A ASN 4.8 0.7 - - - +
42A VAL 3.9 0.6 - - - +
43A ALA* 3.2 4.2 - - - +
44A TYR* 2.8 69.5 + - + +
130A GLU* 2.9 17.7 + - - +
142A VAL* 3.7 10.4 - - - +
143A TYR* 1.3 76.6 + - - +
145A VAL* 1.3 69.3 + - - +
146A THR 4.3 0.2 - - - -
172A LYS* 3.4 28.9 - - + -
173A VAL 3.3 6.3 - - - +
174A ILE* 3.6 10.2 - - + +
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Residues in contact with VAL 145 (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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9A CYS* 5.7 4.0 - - + -
14A PRO* 3.8 28.7 - - + -
41A TRP* 4.1 8.5 - - + -
42A VAL 3.3 11.4 - - - +
43A ALA* 4.4 10.1 - - + -
143A TYR 5.9 0.4 - - - -
144A THR* 1.3 79.4 - - - +
146A THR* 1.3 64.4 + - - +
171A TRP* 3.4 26.8 - - + -
172A LYS* 3.5 1.2 - - - -
173A VAL* 2.9 38.4 + - + +
175A PHE* 6.5 0.4 - - + -
218A ILE* 4.4 18.6 - - + -
219A TRP* 4.9 10.3 - - + +
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Residues in contact with THR 146 (chain A).
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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41A TRP* 3.3 5.2 - - - +
42A VAL* 2.8 41.7 + - + +
44A TYR* 4.0 10.5 - - + -
90A GLN* 3.6 39.3 + - + +
123A TRP* 3.4 20.8 - - - -
145A VAL* 1.3 76.1 - - - +
147A GLY* 1.3 58.3 + - - +
170A TYR* 6.1 0.3 - - - -
171A TRP* 2.7 26.7 + - - -
172A LYS* 4.2 12.8 - - - -
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Residues in contact with GLY 147 (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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40A ASN 3.9 2.5 - - - -
41A TRP* 4.5 0.7 - - - -
90A GLN* 3.3 10.8 - - - -
146A THR* 1.3 80.7 + - - +
148A PRO* 1.3 69.4 - - - +
170A TYR* 3.3 6.5 - - - +
171A TRP* 2.9 48.2 + - - +
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Residues in contact with PRO 148 (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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38A PHE* 5.1 0.9 - - + -
39A ALA 3.2 23.8 - - - +
40A ASN* 3.6 9.5 - - - +
90A GLN* 3.9 9.0 - - - +
147A GLY* 1.3 86.3 - - - +
149A LEU* 1.3 61.9 + - - +
150A TYR* 3.2 33.4 - - + +
167A PRO* 3.6 30.1 - - + -
169A ALA 3.4 6.7 - - - +
170A TYR* 4.2 7.0 - - + -
171A TRP* 3.3 15.4 + - - -
214A THR* 4.2 4.5 - - - +
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Residues in contact with LEU 149 (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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148A PRO* 1.3 74.3 - - - +
150A TYR* 1.3 65.6 + - - +
151A GLU* 3.7 15.5 - - - +
167A PRO* 3.3 6.9 - - - +
168A SER* 2.9 28.2 + - - +
169A ALA* 2.9 20.7 + - + +
171A TRP* 4.0 11.9 - - + -
189A LEU* 3.7 27.6 - - + -
210A ILE* 4.9 1.3 - - + +
213A ARG* 3.5 48.5 - - + +
214A THR* 3.3 33.9 - - + -
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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