Contacts of the strand formed by residues 170 - 174 (chain F) in PDB entry 4IGM
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 170 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LEU* 5.6 1.1 - - - -
139F PRO 3.2 18.7 + - - -
140F GLY* 3.1 4.1 - - - -
141F VAL 2.9 23.8 + - - -
168F LYS 3.7 4.0 + - - -
169F CYS* 1.3 77.6 - - - +
171F LEU* 1.3 60.9 + - - +
219F LYS* 3.5 15.0 - - - +
327F PHE* 2.5 50.1 + - - -
328F LEU* 3.7 8.1 - - - -
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F MET* 4.7 6.1 - - + -
141F VAL* 3.2 35.4 - - + +
143F ILE* 4.0 29.2 - - + -
160F VAL* 6.0 1.8 - - + -
161F TYR* 4.0 27.8 - - + -
164F ALA* 4.1 18.4 - - + -
169F CYS* 4.3 3.8 - - - +
170F SER* 1.3 78.4 - - - +
172F PHE* 1.3 60.0 + - - +
173F VAL* 3.9 0.7 - - + -
206F MET* 5.3 1.3 - - + -
218F LEU* 4.4 15.3 - - + -
219F LYS 2.9 14.9 + - - +
220F VAL* 3.3 14.7 - - + +
221F CYS 2.8 27.9 + - - +
327F PHE* 3.6 5.4 - - - -
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Residues in contact with PHE 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 4.5 18.4 - - + -
6F HIS* 3.7 36.6 - + + -
74F SER* 5.0 1.3 - - - -
114F LEU* 4.2 24.0 - - + +
141F VAL 3.0 11.1 + - - +
142F GLN* 3.3 24.7 - - + +
143F ILE* 2.8 26.7 + - - +
171F LEU* 1.3 73.6 - - - +
173F VAL* 1.3 60.1 + - - +
174F HIS* 3.7 24.8 + + + -
221F CYS* 3.4 32.3 - - + -
223F ALA* 3.9 24.2 - - + -
265F ASP* 4.3 4.7 - - + -
327F PHE* 4.6 5.2 - - + -
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Residues in contact with VAL 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F ILE* 3.3 23.1 - - + -
144F GLY 3.9 3.1 - - - +
145F THR* 3.5 36.6 - - + -
152F LEU* 4.2 12.8 - - + -
171F LEU* 4.9 2.7 - - + +
172F PHE* 1.3 75.0 - - - +
174F HIS* 1.3 61.3 + - - +
175F PRO* 4.1 1.0 - - - +
199F THR* 5.5 0.8 + - + +
202F ALA* 4.4 0.4 - - + -
206F MET* 5.0 1.8 - - + -
220F VAL* 4.0 24.2 - - + -
221F CYS 2.8 8.9 + - - +
222F PHE* 3.8 26.1 - - + -
223F ALA* 3.2 26.7 + - - +
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Residues in contact with HIS 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F HIS* 3.0 16.3 + + - -
8F HIS* 3.7 7.9 - + - -
77F PRO* 3.4 21.2 - - + +
80F PHE* 4.2 6.5 - - + -
142F GLN* 3.8 15.5 - - + +
143F ILE 2.8 13.7 + - - +
144F GLY* 3.2 8.0 - - - -
145F THR* 3.1 18.5 + - - -
172F PHE* 3.7 16.2 - + + -
173F VAL* 1.3 75.1 - - - +
175F PRO* 1.3 94.2 + - + +
176F TRP* 3.4 1.7 + + - -
195F MET* 3.7 19.7 - - + -
223F ALA* 4.3 0.7 - - + -
224F HIS* 4.5 0.4 - - - -
401F ZN 2.2 37.2 - - - -
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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
------------------------------------------------------------
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