Contacts of the strand formed by residues 174 - 179 (chain C) in PDB entry 1I3R
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 LEU 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PRO 4.1 13.2 - - - +
88C GLU* 5.2 0.4 - - - -
89C VAL* 3.4 36.8 - - + +
163C CYS 3.7 1.9 - - - +
164C GLU* 3.4 2.0 - - - -
165C VAL* 2.7 44.0 + - - +
170C LEU* 3.9 25.3 - - + +
172C GLU* 3.3 3.6 + - + +
173C PRO* 1.3 71.9 - - - +
175C ARG* 1.3 62.1 + - - +
176C LYS* 4.2 21.9 - - - +
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Residues in contact with ARG 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 3.8 23.8 - - - +
125C GLY* 5.8 4.8 - - - -
162C ASP* 4.1 32.2 + - + +
163C CYS 3.5 8.1 - - - +
164C GLU* 3.2 33.2 + - + +
173C PRO 3.8 4.4 + - - +
174C LEU* 1.3 78.4 - - - +
176C LYS* 1.3 73.2 + - - +
177C HIS* 4.4 0.6 + - + -
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Residues in contact with LYS 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B SER 5.8 1.4 + - - -
89C VAL* 3.4 44.2 - - + +
90C THR* 5.0 0.7 - - - -
91C VAL* 3.7 25.8 - - + +
162C ASP* 3.3 7.7 - - - -
163C CYS 3.0 33.5 + - - +
174C LEU* 4.2 25.7 - - + +
175C ARG* 1.3 81.6 + - - +
177C HIS* 1.3 61.8 + - - +
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Residues in contact with HIS 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 5.0 3.9 - - - +
160C PHE* 3.4 40.6 - + + -
161C TYR 3.2 6.1 + - - -
162C ASP* 2.8 25.2 + - - +
175C ARG* 4.4 1.1 + - + -
176C LYS* 1.3 76.2 - - - +
178C TRP* 1.3 75.1 + - - +
179C GLU* 2.9 33.2 + - + +
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Residues in contact with TRP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 3.8 41.3 - - + -
92C LEU* 4.5 8.6 - - - +
93C SER* 4.6 5.4 - - - +
97C VAL* 4.1 26.0 - - + -
105C LEU* 3.8 18.3 - - + +
153C PHE* 3.8 32.8 - + - -
155C PRO* 6.3 0.2 - - + -
159C ASP 5.6 0.2 - - - -
160C PHE* 3.6 0.2 - - - -
161C TYR* 2.6 62.4 + + + +
177C HIS* 1.3 81.8 - - - +
179C GLU* 1.3 96.2 + - - +
180C PHE* 3.7 18.2 - - + -
181C GLU 5.8 0.2 - - - -
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Residues in contact with GLU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ASP 4.2 5.8 - - - +
160C PHE* 3.9 16.0 - - + +
177C HIS* 2.9 29.8 + - + +
178C TRP* 1.3 98.1 + - - +
180C PHE* 1.3 72.9 + - - +
181C GLU* 3.6 4.9 + - - +
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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