Contacts of the strand formed by residues 168 - 172 (chain P) in PDB entry 1G3I
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 168 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P GLY 3.1 21.3 + - - -
17P ASP 4.3 0.7 + - - -
30P ASN 4.9 4.5 - - - +
31P ALA 4.6 5.6 - - - +
32P ARG* 4.0 27.8 - - + +
33P LYS 3.8 20.3 + - - -
34P VAL* 3.7 19.6 + - - +
166P ASN* 5.5 4.3 - - - +
167P PHE* 1.3 79.3 - - - +
169P ILE* 1.3 62.1 + - - +
170P GLU* 5.4 4.3 - - - -
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Residues in contact with ILE 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P VAL* 3.1 33.7 - - + -
14P VAL 3.8 1.3 - - - -
15P GLY* 3.9 19.5 - - - -
146P HIS* 4.0 23.7 + - + +
149P VAL* 3.9 5.6 - - + +
150P GLU* 3.7 43.1 - - + +
153P LEU* 4.8 4.9 - - + -
167P PHE* 4.9 10.1 - - + +
168P THR* 1.3 80.2 - - - +
170P GLU* 1.3 70.7 + - - +
171P GLU* 4.4 1.0 + - - +
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Residues in contact with GLU 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P VAL* 3.4 1.7 - - - +
14P VAL 2.9 30.7 + - - +
34P VAL* 4.3 29.4 - - + +
35P ARG* 6.0 0.2 - - - -
36P ARG* 3.6 34.8 + - + +
43P LEU* 3.4 30.5 - - + +
168P THR* 5.3 4.4 - - - +
169P ILE* 1.3 84.1 - - - +
171P GLU* 1.3 61.4 + - - +
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Residues in contact with GLU 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P GLN* 3.2 26.8 + - - -
12P VAL 3.1 12.8 - - - +
13P VAL* 3.8 13.0 - - + +
36P ARG* 3.0 24.0 + - - +
43P LEU* 4.0 0.7 - - - -
146P HIS* 3.9 35.1 + - + +
169P ILE 5.6 0.7 - - - +
170P GLU* 1.3 76.9 + - - +
172P LEU* 1.3 69.1 + - - +
173P PRO* 4.1 8.2 - - - +
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Residues in contact with LEU 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P GLY 4.0 4.3 - - - +
11P GLN* 3.0 16.9 - - - +
12P VAL* 2.9 26.4 + - + +
36P ARG* 3.5 22.0 - - - +
40P GLY 4.0 14.4 - - - +
41P LYS 3.5 23.8 - - - +
42P VAL 5.6 0.2 - - - -
43P LEU* 3.6 22.2 - - + -
98P ALA 4.0 1.1 - - - +
99P ASP* 3.6 22.0 - - - -
100P GLU* 3.8 15.4 - - + +
171P GLU* 1.3 83.8 - - - +
173P PRO* 1.4 72.2 - - + +
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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