Contacts of the strand formed by residues 183 - 189 (chain D) in PDB entry 1O94
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 183 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C HIS 4.9 2.2 + - - -
143C ALA* 6.4 0.2 - - - -
172C VAL* 3.7 17.2 - - - +
173C GLU 3.2 15.7 - - - -
174C ILE* 4.0 13.5 - - - +
175C ASN* 5.4 0.7 - - - +
71D ASP* 3.4 17.7 + - - +
72D PRO* 4.0 17.5 - - - +
73D ASP* 4.7 0.7 + - - -
181D SER* 3.1 21.0 + - - +
182D ARG* 1.3 82.2 - - - +
184D GLN* 1.3 72.1 + - - +
185D ASN* 5.2 1.4 + - - -
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Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C VAL* 3.4 2.3 - - - -
173C GLU* 2.8 46.8 + - + +
66D SER* 6.0 2.2 - - - -
180D GLN* 3.1 35.9 + - - +
181D SER* 5.1 1.2 - - - -
183D SER* 1.3 79.7 + - - +
185D ASN* 1.3 70.2 + - - +
186D LYS* 3.4 22.0 + - - +
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Residues in contact with ASN 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLN* 3.6 25.3 + - - +
171C GLU 3.8 4.0 - - - -
172C VAL* 3.7 20.5 - - - +
67D SER* 4.3 11.3 - - - -
69D ASP* 3.9 12.9 + - - +
70D PHE 2.8 32.0 + - - +
71D ASP* 4.4 9.3 + - - +
72D PRO* 5.7 1.2 - - - +
183D SER* 5.2 1.4 + - - -
184D GLN* 1.3 79.5 + - - +
186D LYS* 1.3 69.7 + - - +
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Residues in contact with LYS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C VAL* 5.9 2.0 - - + -
170C GLN* 4.8 3.6 - - - +
171C GLU* 2.8 39.0 + - + +
172C VAL 4.7 0.2 - - - -
173C GLU* 4.3 27.2 + - + +
184D GLN* 3.8 25.8 + - - +
185D ASN* 1.3 89.2 - - - +
187D ASP* 1.3 71.2 + - + +
188D TYR* 4.1 3.3 + - - -
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Residues in contact with ASP 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLN* 3.7 2.6 - - - +
171C GLU* 3.0 30.7 + - + +
186D LYS* 1.3 86.1 - - - +
188D TYR* 1.3 71.0 + - - +
189D VAL* 4.1 5.2 + - + +
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Residues in contact with TYR 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ARG* 5.6 1.4 + - - -
164C LEU* 3.6 25.8 - - + -
168C MET* 4.1 11.7 - - + -
169C LEU 3.3 13.5 - - - -
170C GLN* 3.4 30.5 + - + -
10D ARG* 3.8 15.2 + - + +
11D ARG* 3.5 52.5 + - + +
69D ASP* 2.7 33.2 + - + +
186D LYS 5.4 3.1 - - - -
187D ASP* 1.3 82.3 - - - +
189D VAL* 1.3 64.4 + - - +
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ARG* 3.7 41.7 - - - +
168C MET* 3.7 19.1 - - - +
169C LEU* 2.7 52.2 + - + +
171C GLU* 4.8 5.4 - - + -
11D ARG* 6.1 0.4 - - - -
187D ASP* 4.4 10.1 - - + +
188D TYR* 1.3 79.2 - - - +
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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