Contacts of the strand formed by residues 56 - 62 (chain B) in PDB entry 1TYG
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 VAL 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B GLN* 3.2 36.1 - - + +
35B GLU* 3.4 2.1 - - - +
36B ARG* 3.1 4.3 - - - -
37B ASN* 2.8 56.0 + - + +
38B LYS* 4.8 2.6 + - + +
55B ASP* 1.3 79.3 - - - +
57B ILE* 1.3 66.4 + - - +
58B GLU* 5.6 5.8 - - + -
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.5 6.7 - - + -
3B GLN 2.8 24.2 + - - +
4B LEU* 3.5 18.6 - - + -
5B ASN 3.1 14.1 + - - -
6B GLY 4.7 0.2 + - - -
18B ILE* 5.0 7.0 - - + -
21B LEU* 4.2 13.7 - - + -
34B VAL* 3.9 10.5 - - + -
35B GLU 3.2 9.2 - - - +
36B ARG* 4.5 13.5 - - + -
51B LEU* 4.1 19.1 - - + -
55B ASP* 3.5 28.0 - - - +
56B VAL* 1.3 78.4 - - - +
58B GLU* 1.3 69.9 + - - +
59B ILE* 3.7 28.0 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 2.4 57.7 + - - +
183A ARG* 4.2 13.9 + - - +
5B ASN* 3.3 10.9 - - - -
6B GLY* 4.0 1.9 + - - -
33B ILE 3.7 1.6 - - - +
34B VAL* 3.6 3.8 - - - +
35B GLU* 2.9 56.4 + - + +
56B VAL* 5.6 6.1 - - + -
57B ILE* 1.3 75.3 - - - +
59B ILE* 1.3 62.4 + - - +
60B VAL* 4.1 8.4 + - + +
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 3.5 2.9 - - - -
147A MET* 2.8 38.9 + - + -
149A ILE* 4.0 14.8 - - + -
4B LEU* 4.8 10.3 - - + -
5B ASN* 2.6 22.4 + - - +
21B LEU* 5.2 9.2 - - + -
22B LEU* 3.7 22.0 - - + -
25B TYR* 5.9 2.7 - - + -
27B LEU* 3.9 13.5 - - + -
32B VAL* 3.8 24.2 - - + -
33B ILE 3.7 3.4 - - - +
34B VAL* 3.5 17.5 - - + -
57B ILE* 3.7 14.3 - - + -
58B GLU* 1.3 71.8 - - - +
60B VAL* 1.3 66.3 + - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.5 22.7 - - + -
145A ARG 3.9 2.5 - - - +
146A ARG* 3.6 20.9 - - - +
147A MET* 3.6 6.1 - - - +
183A ARG* 5.0 5.6 - - - +
187A LEU* 4.3 23.3 - - + -
32B VAL* 3.1 7.4 - - - +
33B ILE* 2.7 59.9 + - + +
58B GLU* 4.5 15.3 - - + +
59B ILE* 1.3 80.8 - - - +
61B HIS* 1.3 61.3 + - - +
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ALA 3.6 0.7 - - - +
144A VAL* 3.7 4.8 - - - -
145A ARG 2.9 42.1 + - - +
146A ARG 4.0 3.2 + - - -
147A MET* 3.5 38.5 - - + -
148A ASN* 4.5 4.3 + - + +
154A GLN 6.0 1.1 - - - -
156A ASN* 3.8 29.1 + - + +
159A GLU* 4.8 2.2 + - - -
30B LYS* 5.4 2.0 + - - -
31B ILE 3.7 20.4 + - - +
32B VAL* 4.3 2.9 - - + -
33B ILE* 4.4 7.0 - - - -
60B VAL* 1.3 80.9 - - - +
62B PHE* 1.3 64.0 + - - +
63B VAL* 3.2 22.3 - - + +
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Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PHE* 3.9 29.3 - + + -
143A ALA 3.1 5.6 - - - -
144A VAL* 3.9 15.0 - - + -
156A ASN* 3.1 23.2 + - - +
158A LEU* 3.5 35.0 + - + +
168A LEU* 5.4 5.2 - - + -
170A PRO* 4.0 12.8 - - + -
188A ALA* 3.6 32.3 - - + -
191A SER* 3.5 39.5 - - - -
193A LEU* 4.8 2.0 - - + -
194A CYS* 4.3 5.6 - - - -
31B ILE* 4.6 9.6 - - + -
33B ILE* 3.9 12.6 - - + -
61B HIS* 1.3 71.7 - - - +
63B VAL* 1.3 68.8 + - - +
64B GLY 4.2 0.7 - - - -
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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