Contacts of the strand formed by residues 161 - 166 (chain G) 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 TYR 161 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G VAL* 6.0 0.4 - - + -
105G LEU* 3.5 19.7 - - + -
121G TRP* 5.2 2.9 - - + -
122G LEU 3.3 4.7 - - - +
123G ARG* 3.4 51.3 + - + -
151G LEU* 3.7 28.7 - - + -
153G PHE* 3.6 34.3 - + + +
154G LEU 4.1 6.6 + - - -
155G PRO* 6.1 0.7 - - + -
156G SER 5.9 2.0 - - - -
159G ASP* 4.0 24.6 + - + +
160G PHE* 1.3 80.7 - - - +
162G ASP* 1.3 70.4 + - - +
176G LYS 4.5 0.2 - - - -
177G HIS* 3.4 2.3 + - - -
178G TRP* 2.5 62.7 + + + +
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Residues in contact with ASP 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 5.9 0.2 - - - -
120G THR 3.8 0.2 - - - +
121G TRP* 3.6 8.2 - - - -
122G LEU* 2.7 54.0 + - + +
125G GLY* 5.2 2.3 + - - -
160G PHE* 4.0 14.9 - - - -
161G TYR* 1.3 76.5 - - - +
163G CYS* 1.3 59.7 + - - +
164G GLU 4.0 0.2 - - - -
175G ARG* 3.7 35.6 + - + +
176G LYS 3.2 5.3 - - - +
177G HIS* 3.0 41.4 + - - +
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Residues in contact with CYS 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 3.8 17.6 - - + +
107G CYS* 2.0 51.6 - - + -
119G VAL* 3.8 20.4 - - - -
120G THR 3.6 3.1 - - - -
121G TRP* 4.1 12.1 - - + -
162G ASP* 1.3 73.5 - - - +
164G GLU* 1.3 61.8 + - - +
165G VAL* 3.8 8.0 + - - +
174G LEU 3.4 3.8 - - - +
175G ARG* 4.5 0.9 - - - -
176G LYS* 3.0 30.8 + - + +
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Residues in contact with GLU 164 (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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118G ASN 3.5 1.9 - - - +
119G VAL* 3.3 5.0 - - - -
120G THR* 2.8 53.7 + - - +
122G LEU* 4.0 13.9 - - + -
162G ASP 4.0 0.6 - - - -
163G CYS* 1.3 72.7 - - - +
165G VAL* 1.3 62.1 + - - +
166G ASP* 4.1 1.3 + - + +
173G PRO* 4.0 26.1 - - + +
174G LEU 3.2 10.5 - - - +
175G ARG* 2.9 38.5 + - - +
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Residues in contact with VAL 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PRO* 4.1 25.4 - - + -
89G VAL* 3.8 28.0 - - + -
109G ILE* 4.0 27.1 - - + -
117G VAL* 4.5 6.3 - - + -
118G ASN 3.4 5.8 - - - +
119G VAL* 4.5 2.2 - - + -
163G CYS* 3.9 23.1 - - - +
164G GLU* 1.3 76.7 - - - +
166G ASP* 1.3 68.6 + - - +
170G LEU* 3.4 7.0 - - + +
173G PRO* 4.5 1.1 - - - -
174G LEU* 2.7 42.2 + - + +
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Residues in contact with ASP 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G VAL* 3.5 5.9 - - - +
118G ASN* 2.8 50.6 + - + +
164G GLU* 4.1 1.3 + - + +
165G VAL* 1.3 75.8 - - - +
167G HIS* 1.3 71.1 + - - +
170G LEU* 4.2 3.7 - - - +
172G GLU 4.5 2.3 - - - -
173G PRO* 3.7 38.0 - - + +
1L NAG 3.4 26.0 - - - +
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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