Contacts of the strand formed by residues 182 - 187 (chain E) in PDB entry 1SV6
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 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180E ASN 3.3 0.6 + - - -
181E CYS* 1.3 73.7 - - - +
183E MET* 1.3 59.3 + - - +
184E LYS* 4.3 10.2 - - + +
195E GLY 3.7 5.4 - - - +
196E ARG* 4.2 17.0 - - - +
248E HIS 3.3 3.8 - - - +
249E ILE* 3.4 2.1 - - - -
250E GLU* 2.8 49.4 + - + +
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Residues in contact with MET 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ALA* 3.5 36.1 - - + +
181E CYS 5.2 0.2 - - - +
182E ALA* 1.3 72.3 - - - +
184E LYS* 1.3 72.2 + - - +
185E MET* 3.6 18.4 - - + -
193E SER* 3.9 6.7 - - - +
194E SER* 3.0 54.9 - - - +
195E GLY 2.6 22.3 + - - +
196E ARG* 4.5 1.1 - - - +
233E LEU* 4.0 23.1 - - + -
234E GLY* 3.6 27.1 - - - +
235E PRO 5.5 0.2 - - - +
247E ALA* 5.0 0.2 - - + -
248E HIS 3.2 8.3 - - - +
249E ILE* 4.4 4.5 - - + -
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Residues in contact with LYS 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E ALA* 5.1 8.5 - - + -
183E MET* 1.3 88.8 - - - +
185E MET* 1.3 59.9 + - - +
186E THR* 5.0 6.0 - - + +
191E GLU* 2.6 42.3 + - - -
193E SER 3.7 3.4 - - - -
194E SER* 4.1 7.9 + - - -
246E GLU 3.7 1.2 - - - +
247E ALA* 3.3 2.1 - - - -
248E HIS* 3.0 42.8 + - + +
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Residues in contact with MET 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ILE* 3.1 42.2 - - + +
105E GLU* 4.0 9.0 - - - -
106E ALA* 4.2 8.5 - - + +
137E LEU* 3.5 29.2 - - - -
183E MET* 3.6 13.8 - - + -
184E LYS* 1.3 71.6 - - - +
186E THR* 1.3 73.3 + - - +
191E GLU* 3.6 3.1 - - - +
192E VAL* 2.8 24.6 + - + +
193E SER* 2.9 34.3 + - - +
235E PRO 4.5 1.8 - - - +
237E VAL* 4.2 6.1 - - + -
245E PHE* 4.3 6.7 - - + -
246E GLU 3.3 11.9 - - - +
247E ALA* 4.1 3.1 - - + -
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Residues in contact with THR 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E LYS* 5.0 6.7 - - + +
185E MET* 1.3 80.8 - - - +
187E ARG* 1.3 61.1 + - - +
188E ASN 4.1 0.2 - - - -
189E ASN* 4.0 15.4 + - - +
190E GLU 3.3 17.5 - - - -
191E GLU* 3.6 22.2 - - + +
192E VAL* 3.8 3.6 - - - -
244E ARG 3.8 0.5 + - - +
245E PHE* 3.1 9.5 - - - +
246E GLU* 2.9 46.7 + - - +
248E HIS* 5.7 5.5 + - + -
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Residues in contact with ARG 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E THR* 1.3 73.3 - - - +
188E ASN* 1.3 85.9 + - - +
190E GLU* 2.9 54.4 + - - +
192E VAL* 3.8 22.2 - - + +
237E VAL* 4.7 6.5 - - - +
238E ALA* 3.5 21.2 + - - +
240E ASN* 3.9 13.5 + - - -
243E ASP* 3.2 29.6 - - + -
244E ARG 3.5 4.3 - - - +
245E PHE* 3.7 22.7 - - + -
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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