Contacts of the strand formed by residues 189 - 194 (chain G) in PDB entry 1IB1
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 THR 189 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G MET* 3.2 3.6 - - - -
160G CYS 2.8 33.9 + - - -
161G GLU* 4.9 0.2 - - - +
162G ASP* 3.1 27.6 + - - +
165G VAL* 4.1 22.2 - - + -
175G PRO* 4.6 7.2 - - + -
176G ALA 4.6 1.8 - - - +
177G GLY* 3.5 22.8 - - - +
178G PRO* 4.5 1.0 - - - +
179G CYS* 4.3 1.3 - - - -
188G PHE* 1.3 73.2 - - - +
190G GLU* 1.3 73.7 + - - +
191G MET* 4.3 6.6 - - - +
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Residues in contact with GLU 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G ARG* 3.4 25.5 + - - +
104G LEU* 3.0 47.2 + - + +
158G LEU 3.8 7.6 - - - +
159G MET* 4.5 0.7 - - - +
175G PRO* 3.6 4.9 - - - +
176G ALA* 2.7 36.2 + - + -
177G GLY 2.8 18.2 + - - +
179G CYS* 3.4 27.3 - - + +
180G ALA 4.3 0.3 + - - -
188G PHE 4.1 1.0 + - - -
189G THR* 1.3 75.4 - - - +
191G MET* 1.3 58.9 + - - +
192G HIS* 2.8 31.8 + - + +
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Residues in contact with MET 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G ALA 3.9 0.2 - - - +
157G VAL* 3.4 2.8 - - - +
158G LEU* 2.8 52.9 + - + +
160G CYS* 3.9 10.8 - - - -
165G VAL* 3.5 41.7 - - + +
168G TYR* 3.4 27.6 - - + -
169G GLN* 4.1 9.2 - - + -
173G PHE* 3.7 29.9 - - + -
174G HIS 3.2 4.7 - - - -
175G PRO* 4.0 13.2 - - - -
189G THR* 4.3 2.0 - - - +
190G GLU* 1.3 84.8 - - - +
192G HIS* 1.3 71.0 + - - +
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Residues in contact with HIS 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G GLU* 3.6 32.8 + - - -
103G ARG* 4.1 8.3 - - - -
155G ARG* 4.1 17.6 + - - -
156G ALA 3.5 2.7 - - - -
157G VAL* 3.3 19.2 - - + +
172G GLY 3.7 1.7 - - - +
173G PHE* 3.2 1.6 - - - -
174G HIS* 2.8 43.8 + - + +
176G ALA* 3.5 22.6 - - + +
190G GLU* 2.8 30.3 + - + +
191G MET* 1.3 87.0 - - - +
193G CYS* 1.3 59.4 + - - +
194G SER 4.2 0.8 + - - -
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Residues in contact with CYS 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LEU* 4.5 9.0 - - - -
155G ARG* 3.2 5.0 - - - +
156G ALA* 2.8 38.8 + - + +
171G PHE 3.7 23.3 - - - -
172G GLY* 3.8 13.9 - - - -
173G PHE* 3.4 34.5 - - + -
192G HIS* 1.3 74.3 - - - +
194G SER* 1.3 76.3 + - - +
195G LEU* 3.9 8.5 - - - +
24H PRO* 6.1 1.6 - - - -
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Residues in contact with SER 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ARG 4.0 5.9 + - - -
155G ARG* 4.3 6.2 - - - +
172G GLY 4.8 2.2 + - - -
174G HIS* 5.7 2.7 - - - -
192G HIS 4.2 0.6 + - - -
193G CYS* 1.3 84.5 - - - +
195G LEU* 1.3 67.7 + - - +
196G ARG 4.4 3.6 + - - -
24H PRO* 5.7 0.3 - - - +
26H ARG* 3.7 19.1 + - - -
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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