Contacts of the strand formed by residues 153 - 160 (chain D) in PDB entry 1GN2
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 ILE 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B LEU* 4.2 20.1 - - + +
152B GLY* 3.4 16.9 + - - +
129D GLY* 4.4 5.4 - - - -
130D TRP 3.3 19.1 - - - +
131D ASP* 3.4 26.2 - - + +
138D LEU* 5.0 0.2 - - + -
140D PHE* 3.6 33.2 - - + -
149D PHE* 5.5 0.4 - - + -
150D PRO* 3.8 40.1 + - + +
151D LEU 3.3 2.7 - - - +
152D GLY* 1.3 77.4 - - - +
154D VAL* 1.3 70.7 + - - +
155D PRO* 3.4 8.7 - - - +
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLY* 5.2 1.3 - - - -
129D GLY* 3.0 4.9 - - - -
130D TRP* 2.6 58.2 + - + +
132D THR* 4.1 13.0 - - + -
152D GLY 4.4 2.7 - - - +
153D ILE* 1.3 74.2 - - - +
155D PRO* 1.3 77.8 - - + +
156D LEU* 3.6 4.5 + - + +
193D ARG* 5.3 2.2 - - + +
197D ALA* 4.2 26.2 - - + -
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Residues in contact with PRO 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 4.3 34.1 - - + +
152B GLY* 4.2 12.3 - - - +
74D VAL* 5.4 1.6 - - + -
78D ILE* 3.7 27.5 - - + +
127D ALA* 6.1 0.7 - - + -
128D LEU 3.9 5.2 - - - +
129D GLY* 4.3 1.6 - - - -
153D ILE* 3.4 11.6 - - + +
154D VAL* 1.3 94.3 - - + +
156D LEU* 1.3 67.4 + - - +
158D LEU* 4.6 9.2 - - + -
193D ARG* 4.0 15.2 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ILE* 4.6 3.0 - - - +
82D ASN* 3.4 11.2 + - - -
95D LEU* 5.5 1.1 - - + -
128D LEU* 2.9 32.0 + - + +
129D GLY 4.3 3.8 - - - -
130D TRP* 4.3 2.9 - - + -
137D LEU* 3.6 31.9 - - + -
154D VAL* 3.9 13.5 - - + +
155D PRO* 1.3 82.1 - - - +
157D LEU* 1.3 59.4 + - - +
190D VAL* 4.1 14.5 - - + +
193D ARG* 3.3 54.4 - - + +
194D TYR* 3.8 19.5 - - + +
197D ALA* 4.2 10.5 - - + -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ASN* 3.2 26.7 - - + +
109D PHE* 4.4 10.1 - - + -
113D PHE* 4.2 17.0 - - + -
127D ALA* 3.2 1.0 - - - -
128D LEU* 2.8 41.0 + - + -
156D LEU* 1.3 80.6 - - - +
158D LEU* 1.3 69.5 + - - +
181D PHE* 3.9 23.6 - - + -
182D TRP* 4.4 14.1 - - + -
185D VAL* 4.1 9.0 - - + -
187D TRP* 4.2 27.6 - - + -
190D VAL* 4.0 19.3 - - + -
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 4.3 13.7 - - + -
75D ASN* 3.9 41.3 - - + +
78D ILE* 4.3 21.3 - - + -
79D TRP* 3.5 17.8 - - + -
82D ASN* 2.9 13.8 + - - +
113D PHE* 4.5 2.9 - - - -
125D TRP* 3.6 24.5 - - + -
126D ALA 3.3 3.8 - - - -
127D ALA* 3.0 33.0 - - + -
128D LEU 4.5 0.7 - - - +
155D PRO* 4.6 8.7 - - + -
157D LEU* 1.3 84.0 - - - +
159D LEU* 1.3 62.8 + - - +
160D ASP 4.1 0.7 - - - -
181D PHE* 3.8 10.5 - - - -
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TRP* 3.8 3.8 - - + -
113D PHE* 3.8 25.8 - - + -
114D HIS* 6.1 1.1 - - - -
117D ALA* 4.1 15.7 - - + -
125D TRP* 3.3 4.3 - - - -
126D ALA* 2.9 29.7 + - + +
158D LEU* 1.3 75.4 - - - +
160D ASP* 1.3 66.1 + - - +
161D MET* 3.3 12.5 + - - +
177D PHE* 3.5 35.4 - - + -
178D ALA* 4.2 19.1 - - + +
181D PHE* 3.7 39.3 - - + -
182D TRP* 5.7 0.7 - - - +
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D HIS* 2.9 14.6 + - - -
76D HIS* 3.6 1.6 + - - -
79D TRP* 3.6 16.4 - - + -
125D TRP* 3.3 31.7 - - + -
159D LEU* 1.3 70.8 - - - +
161D MET* 1.3 57.4 + - - +
162D TRP* 2.8 41.6 + - - +
164D HIS* 3.4 0.2 + - - -
165D ALA* 3.5 17.2 - - + +
177D PHE* 3.4 23.6 - - - -
999D FE 2.0 31.0 - - - -
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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