Contacts of the strand formed by residues 168 - 172 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16M GLY 3.0 20.8 + - - -
17M ASP 4.3 0.5 + - - -
30M ASN 4.9 4.7 - - - +
31M ALA 4.5 8.5 - - - +
32M ARG* 4.0 25.1 - - + +
33M LYS 3.8 20.8 + - - -
34M VAL* 3.6 19.9 + - - +
166M ASN* 5.4 4.0 - - - +
167M PHE* 1.3 80.5 - - - +
169M ILE* 1.3 63.7 + - - +
170M GLU* 5.4 4.5 - - - -
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Residues in contact with ILE 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M VAL* 3.1 33.9 - - + -
14M VAL 3.8 8.1 - - - +
15M GLY* 3.9 11.7 - - - -
146M HIS* 4.0 24.0 + - + +
149M VAL* 3.9 6.3 - - + +
150M GLU* 3.7 43.1 - - + +
153M LEU* 4.8 4.7 - - + -
167M PHE* 4.9 10.3 - - + +
168M THR* 1.3 81.4 - - - +
170M GLU* 1.3 70.7 + - - +
171M GLU* 4.4 0.9 + - - +
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Residues in contact with GLU 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M VAL* 3.4 2.3 - - - +
14M VAL 2.9 31.4 + - - +
34M VAL* 4.2 30.7 - - + +
35M ARG* 6.0 0.2 - - - -
36M ARG* 3.5 35.9 + - + +
43M LEU* 3.4 28.1 - - + +
168M THR* 5.3 3.8 - - - +
169M ILE* 1.3 83.7 - - - +
171M GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M GLN* 3.2 26.9 + - - +
12M VAL 3.1 12.6 - - - +
13M VAL* 3.8 13.6 - - + +
36M ARG* 3.1 23.7 + - - +
43M LEU* 4.0 0.7 - - - -
146M HIS* 3.9 34.9 - - + +
169M ILE 5.6 0.7 - - - +
170M GLU* 1.3 76.1 + - - +
172M LEU* 1.3 69.3 + - - +
173M PRO* 4.1 8.3 - - - +
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Residues in contact with LEU 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M GLY 4.0 4.2 - - - +
11M GLN* 3.0 17.3 - - - +
12M VAL* 2.9 25.2 + - + +
36M ARG* 3.5 22.7 - - - +
40M GLY 4.0 13.9 - - - +
41M LYS 3.5 23.6 - - - +
42M VAL 5.6 0.2 - - - -
43M LEU* 3.6 24.9 - - + -
98M ALA 4.0 0.7 - - - +
99M ASP* 3.6 22.2 - - - -
100M GLU* 3.8 15.6 - - + +
171M GLU* 1.3 81.8 - - - +
173M PRO* 1.3 70.9 - - + +
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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