Contacts of the strand formed by residues 155 - 163 (chain D) in PDB entry 3G4C
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 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.5 15.9 - - - +
7D ASP* 2.7 23.7 + - - -
8D LYS* 3.2 18.1 + - + -
9D GLY* 3.4 26.4 + - - -
67D LYS* 3.8 19.5 - - + -
68D ALA* 3.4 21.5 - - - -
69D PRO* 3.7 17.5 - - + -
87D LEU* 5.6 1.7 - - - +
94D LEU* 5.6 3.5 - - - +
95D SER 5.5 0.5 - - - +
97D GLU* 2.9 30.6 + - + +
98D PHE 3.5 22.2 - - - -
99D TYR* 3.3 25.4 - - + +
153D ASN 3.3 1.2 + - - -
154D LEU* 1.3 86.5 - - - +
156D THR* 1.3 59.2 + - - +
186D TYR* 3.8 1.1 - - - -
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Residues in contact with THR 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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74A ARG* 4.5 1.7 + - - -
67D LYS* 3.3 6.1 - - - +
68D ALA 2.7 41.4 + - - +
70D ILE* 4.0 19.3 - - + -
73D ALA* 3.9 22.2 - - + -
86D GLU* 2.4 39.4 + - - +
87D LEU* 4.2 12.6 + - - +
154D LEU* 6.2 0.2 - - - -
155D TYR* 1.3 74.3 - - - +
157D ARG* 1.3 67.2 + - - +
158D PHE* 4.7 6.2 - - + -
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Residues in contact with ARG 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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29C VAL* 2.7 34.0 + - + +
30C SER* 4.8 1.2 - - - +
10D PHE* 4.1 12.3 - - - -
65D HIS* 3.3 30.7 + - - +
66D VAL 3.2 5.8 - - - +
67D LYS* 3.7 23.5 - - + +
86D GLU* 3.3 5.9 - - - +
87D LEU* 3.0 61.4 + - + +
156D THR* 1.3 80.2 + - - +
158D PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 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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29C VAL* 3.8 3.1 - - - -
64D PHE 3.8 0.3 - - - +
65D HIS* 3.5 2.9 - - - -
66D VAL* 2.9 71.2 + - + -
68D ALA* 4.3 8.5 - - + -
73D ALA* 4.0 17.3 - - + -
76D TRP* 3.8 29.4 - + + -
77D PHE* 3.7 36.8 - + + -
84D TYR* 4.2 2.9 - + - -
85D ASN 3.0 17.0 - - - +
86D GLU* 3.8 8.1 - - + -
156D THR* 4.7 5.2 - - + -
157D ARG* 1.3 80.4 - - - +
159D PHE* 1.3 77.3 + - - +
160D TRP* 4.1 12.3 - - + -
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Residues in contact with PHE 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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22C SER 5.1 2.2 - - - -
25C ARG* 3.6 24.2 - - + -
26C ALA* 3.7 22.7 - - + -
29C VAL* 3.8 9.0 - - + -
30C SER 3.6 32.1 - - - -
31C PHE* 4.0 8.3 - - - -
59C HIS* 3.9 16.8 - + + +
14D VAL* 4.1 26.2 - - + -
63D THR* 3.9 16.6 - - + -
64D PHE 3.3 4.3 - - - -
65D HIS* 3.7 26.9 - + + -
84D TYR* 3.3 7.6 - - - -
85D ASN 2.8 32.4 + - - +
158D PHE* 1.3 81.1 - - - +
160D TRP* 1.3 60.0 + - - +
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Residues in contact with TRP 160 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D PHE 3.8 0.9 - - - +
63D THR* 3.2 1.8 - - - -
64D PHE* 2.8 65.6 + + + +
66D VAL* 4.9 0.2 - - + -
76D TRP* 3.4 41.5 - + - -
79D HIS* 5.1 3.8 - - + -
82D ALA* 3.2 13.4 - - + +
83D SER 3.3 9.2 - - - -
84D TYR* 3.1 40.5 + + - -
158D PHE* 4.1 12.8 - - + -
159D PHE* 1.3 74.2 - - - +
161D THR* 1.3 62.6 + - - +
162D VAL* 3.8 29.8 - - + -
166D SER* 5.6 0.9 - - - -
167D LEU* 3.8 19.5 - - + -
170D PHE* 3.7 31.2 - + + -
190D ILE* 4.0 10.5 - - + -
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Residues in contact with THR 161 (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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17C MET* 3.8 7.9 - - + -
58C GLU 4.3 12.8 - - - +
59C HIS* 2.6 34.1 + - - +
61C VAL* 4.6 1.6 - - + -
61D VAL* 3.6 20.2 - - + -
62D PHE 3.2 14.6 - - - +
63D THR* 2.9 20.8 + - - +
82D ALA* 3.3 6.2 - - - +
83D SER* 2.9 38.7 + - - +
160D TRP* 1.3 70.0 - - - +
162D VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 162 (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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61D VAL* 3.5 4.7 - - - -
62D PHE* 2.9 30.5 + - + +
64D PHE* 3.9 28.0 - - + -
81D ILE 4.2 3.6 - - - +
82D ALA* 4.2 3.8 - - + +
160D TRP* 3.8 38.8 - - + -
161D THR* 1.3 76.7 - - - +
163D ASN* 1.3 73.3 + - - +
166D SER* 3.6 15.3 - - - +
167D LEU* 3.5 24.9 - - + +
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Residues in contact with ASN 163 (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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310B FAD 3.0 30.6 + - - -
83C SER* 4.3 2.4 + - - -
58D GLU* 3.4 30.0 + - - +
60D ILE 3.1 15.9 - - - +
61D VAL* 4.1 7.6 - - + +
62D PHE* 5.0 1.3 - - - -
81D ILE* 5.0 3.4 + - - +
162D VAL* 1.3 75.5 - - - +
164D ALA* 1.3 52.3 + - - +
165D ARG* 3.2 10.6 + - - +
166D SER* 2.9 32.1 + - - -
167D LEU* 2.8 35.7 + - - +
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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