Contacts of the strand formed by residues 156 - 161 (chain I) in PDB entry 6O81
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 ASP 156 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I MET* 5.3 1.9 - - - +
155I ARG* 1.3 78.7 + - - +
157I PHE* 1.3 63.6 + - - +
158I ILE* 3.8 23.8 + - + +
170I MET* 6.2 1.6 - - + -
171I ALA 3.5 8.3 - - - +
172I ASN* 3.4 19.7 - - - +
196I HIS 3.5 9.7 - - - +
197I THR* 3.7 11.6 - - - +
199I LEU* 2.9 30.6 + - - +
200I VAL* 4.6 7.1 - - - -
201I ASP* 4.7 5.2 + - - +
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Residues in contact with PHE 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.6 28.7 - - + -
231A PHE* 3.6 41.1 - + + -
155I ARG* 4.2 8.7 - - - -
156I ASP* 1.3 72.1 - - - +
158I ILE* 1.3 60.4 + - - +
159I GLY 4.0 0.6 + - - -
169I PHE* 4.5 5.2 - + + -
170I MET* 3.2 4.0 - - - -
171I ALA* 2.9 44.9 + - + +
172I ASN 5.2 0.4 - - - -
173I GLU* 4.0 33.7 - - + -
176I LEU* 6.2 2.0 - - + -
179I GLU 5.5 1.8 - - - -
180I LEU* 5.6 4.5 - - + -
195I PHE* 4.4 17.7 - - + -
196I HIS 3.4 4.7 - - - +
197I THR* 3.3 31.4 - - - -
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Residues in contact with ILE 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I MET* 3.8 33.4 - - + -
156I ASP* 3.9 29.6 - - + +
157I PHE* 1.3 79.3 - - - +
159I GLY* 1.3 64.2 + - - +
160I VAL* 3.8 5.0 + - + +
167I LEU* 4.9 11.0 - - + -
169I PHE 3.5 8.5 - - - +
170I MET* 3.7 22.0 - - + -
171I ALA 4.9 0.2 - - - +
194I ARG 3.6 1.7 - - - +
195I PHE* 3.4 3.7 - - - -
196I HIS* 2.9 37.4 + - - +
199I LEU* 3.8 29.8 - - + -
265I SER* 5.4 3.6 - - - +
267I ILE* 5.8 1.8 - - + -
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Residues in contact with GLY 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I ILE* 1.3 72.3 - - - +
160I VAL* 1.3 59.7 + - - -
167I LEU* 4.0 1.0 - - - +
168I LEU* 2.9 24.6 + - - -
169I PHE 2.8 23.0 + - - +
193I ILE* 3.7 13.0 - - - -
194I ARG 3.4 7.0 - - - -
195I PHE* 3.6 25.3 - - - -
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Residues in contact with VAL 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I ILE* 3.8 6.0 + - + +
159I GLY* 1.3 74.6 - - - -
161I ASP* 1.3 70.4 + - - +
164I GLY* 4.0 28.5 - - - +
165I LYS 4.1 3.1 - - - +
166I ARG 3.3 22.0 - - - +
167I LEU* 3.9 7.9 - - + +
168I LEU* 4.4 1.1 - - - -
193I ILE* 3.6 6.4 - - - -
194I ARG* 2.9 44.0 + - + +
196I HIS* 3.8 24.5 - - + +
265I SER* 4.4 10.1 - - - +
267I ILE* 5.6 7.0 - - + -
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Residues in contact with ASP 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I VAL* 1.3 81.1 - - - +
162I SER* 1.3 80.4 + - - +
163I THR* 3.1 21.7 + - - +
164I GLY* 2.8 22.5 + - - -
166I ARG* 2.9 30.7 + - + +
168I LEU* 3.9 13.2 - - + +
190I HIS* 3.2 39.8 + - + +
191I PRO* 5.9 0.9 - - - +
192I ARG* 3.7 10.2 - - - +
194I ARG* 5.0 0.9 - - - +
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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