Contacts of the helix formed by residues 162 - 171 (chain B) in PDB entry 3SPD
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 ASN 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B LYS* 1.3 83.1 - - - +
163B SER* 1.3 65.2 + - - +
164B ALA* 3.2 12.4 + - - +
165B HIS* 3.0 57.5 + - - +
166B TYR 3.4 1.9 + - - -
211B PHE* 3.3 22.2 - - - -
9E T 5.8 8.5 - - + -
1F G 4.7 5.8 + - - +
3F C 5.3 0.4 + - - -
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASN* 1.3 74.6 - - - +
164B ALA* 1.3 64.5 + - - +
166B TYR* 3.1 2.7 + - - +
167B ILE* 2.9 29.3 + - - +
198B LEU* 3.3 37.3 - - - +
209B ARG* 3.7 33.4 + - - -
211B PHE* 3.6 17.6 - - - +
9E T 4.6 4.0 + - - -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ASN* 3.2 8.1 + - - +
163B SER* 1.3 78.3 - - - +
165B HIS* 1.3 63.7 + - - +
167B ILE* 4.6 0.9 - - - -
168B SER* 2.9 27.5 + - - -
194B PHE* 3.6 20.0 + - + +
209B ARG* 5.5 0.4 - - - +
1F G 3.0 51.1 + - + +
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Residues in contact with HIS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 3.5 19.5 - - + +
159B SER 3.5 17.1 + - - -
160B LEU* 3.8 16.2 - - + -
161B LYS* 3.1 26.9 + - + -
162B ASN* 3.0 40.6 + - - +
164B ALA* 1.3 74.8 - - - +
166B TYR* 1.3 61.5 + - - +
168B SER* 2.7 21.0 + - - -
169B PHE* 3.3 13.8 - + - -
1F G 3.1 22.7 - - - -
2F T 5.2 0.9 - - - -
3F C 2.8 31.5 + - - -
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Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B HIS* 4.2 18.6 - + + -
160B LEU* 4.0 13.2 - - + +
162B ASN 3.4 6.2 + - - +
163B SER* 3.1 7.9 + - - +
165B HIS* 1.3 79.5 - - - +
167B ILE* 1.3 62.6 + - + +
169B PHE* 3.1 12.1 + - - +
170B THR* 2.8 50.4 + - + +
198B LEU* 4.1 11.0 - - + -
199B LYS 2.8 33.9 + - - -
200B CYS* 3.4 3.8 - - - -
201B TRP* 2.8 26.0 + + - +
211B PHE* 4.6 4.9 - - + -
214B LEU* 3.6 29.9 - - + +
218B LEU* 3.9 29.1 - - + +
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B SER 2.9 21.7 + - - +
164B ALA 4.1 2.2 - - - +
166B TYR* 1.3 78.3 - - + +
168B SER* 1.3 61.3 + - - +
169B PHE 3.1 1.4 + - - -
170B THR* 3.7 7.0 - - - +
171B SER* 2.8 47.4 + - - +
193B LEU* 3.8 26.9 - - + +
194B PHE* 3.7 38.1 - - + +
196B GLU* 4.1 7.9 - - + +
197B ASP 5.4 2.2 - - - +
198B LEU* 4.0 18.2 - - + -
209B ARG* 3.9 13.7 - - - +
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B HIS* 3.2 32.9 + - - -
164B ALA 2.9 16.5 + - - -
165B HIS* 2.7 21.0 + - - -
167B ILE* 1.3 76.4 - - - +
169B PHE* 1.3 69.4 + - - +
173B PHE* 3.6 20.6 - - - -
174B PHE* 3.5 12.2 + - - +
194B PHE* 4.0 3.5 - - - -
1F G 3.8 22.1 - - - -
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 3.6 33.4 - - + -
71B HIS* 3.6 17.9 - + - -
134B LYS* 2.9 20.6 + - - +
138B HIS* 3.4 25.6 - + - -
149B HIS* 3.6 26.5 - + - -
151B MET* 3.3 22.0 - - - -
155B HIS* 3.3 25.4 - + + +
165B HIS* 3.3 10.8 - - - -
166B TYR 3.1 4.5 + - - +
167B ILE 3.1 0.6 - - - -
168B SER* 1.3 98.3 + - - +
170B THR* 1.3 59.3 + - - +
171B SER 3.7 1.1 - - - -
174B PHE* 3.6 32.2 - + - +
176B LYS* 5.5 1.6 + - - -
1F G 6.0 0.7 - - - -
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 3.9 4.7 - - - +
155B HIS* 3.6 26.5 - - + +
166B TYR* 2.8 52.2 + - + +
167B ILE* 3.7 4.2 - - - +
169B PHE* 1.3 82.7 - - - +
171B SER* 1.3 61.5 + - - +
174B PHE* 5.3 0.2 - - - -
199B LYS* 5.5 7.2 - - - -
201B TRP* 4.2 17.4 - - + +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 2.8 31.1 + - - +
170B THR* 1.3 80.5 - - - +
172B PRO* 1.3 71.2 - - - +
173B PHE* 2.9 20.5 + - - +
174B PHE* 2.9 26.2 + - - +
193B LEU* 3.5 14.1 - - - +
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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