Contacts of the strand formed by residues 17 - 23 (chain G) in PDB entry 3T30
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 17 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G THR 4.3 0.2 + - - -
16G THR* 1.3 77.0 - - - +
18G LEU* 1.3 73.3 + - + +
118G GLN* 3.3 6.4 - - - -
119G GLU* 2.7 72.4 + - + +
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G THR* 5.5 0.2 - - - +
17G VAL* 1.3 87.0 - - + +
19G TRP* 1.3 60.0 + - - +
47G HIS* 5.5 2.5 - - - +
116G SER* 5.9 0.4 - - - -
117G GLY 3.4 18.4 - - - +
118G GLN* 3.9 13.2 - - + +
119G GLU* 4.8 2.4 - - - +
64H ILE* 3.3 47.3 - - + +
78H VAL* 4.1 25.3 - - + +
80H ILE* 5.7 2.0 - - + -
98H LEU* 4.1 19.1 - - + -
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Residues in contact with TRP 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL 4.5 0.2 - - - +
18G LEU* 1.3 76.2 - - - +
20G GLY* 1.3 68.9 + - - +
21G CYS* 4.0 20.0 - - + -
30G TRP* 4.3 18.1 - + - +
32G PHE* 4.1 20.7 - + + +
44G LEU* 3.7 28.7 - - + -
46G LEU* 4.5 5.6 - - + -
104G PHE* 3.7 29.6 - + - -
115G LEU* 3.9 28.7 - - + -
116G SER* 3.5 11.2 - - - -
117G GLY 2.8 46.2 + - - +
119G GLU* 3.8 31.0 - - + +
78H VAL* 3.5 10.5 - - - +
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Residues in contact with GLY 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G TRP* 1.3 90.8 + - - +
21G CYS* 1.3 62.2 + - - +
30G TRP* 5.2 1.0 + - - -
115G LEU 3.1 13.5 - - - -
77H PRO 6.0 0.7 - - - -
78H VAL* 3.8 19.7 - - - +
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Residues in contact with CYS 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G TRP* 4.0 10.1 - - + -
20G GLY* 1.3 75.6 - - - +
22G GLU* 1.3 62.1 + - - +
23G LEU* 4.2 19.5 - - - -
30G TRP* 3.7 38.4 - - + +
104G PHE* 5.0 3.8 - - - -
113G VAL 3.8 0.2 - - - +
114G PHE* 3.3 7.3 - - - +
115G LEU* 2.8 54.3 + - - +
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Residues in contact with GLU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G CYS* 1.3 76.0 - - - +
23G LEU* 1.3 66.1 + - - +
24G SER* 4.3 4.1 + - - -
27G ARG* 3.8 23.5 + - - +
112G PRO* 3.4 30.4 - - + +
113G VAL 3.4 3.6 - - - +
114G PHE* 3.3 33.2 - - + -
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Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G CYS* 4.2 10.5 - - + -
22G GLU* 1.3 78.4 - - - +
24G SER* 1.3 65.0 + - - +
27G ARG* 3.3 15.5 - - + +
28G ARG 4.2 2.0 - - - +
29G THR 4.0 9.2 - - - +
30G TRP* 3.8 28.7 - - + +
62G VAL* 4.7 8.3 - - + -
104G PHE* 4.2 18.2 - - + +
105G GLN 4.4 1.3 - - - -
106G LEU* 3.9 38.1 - - + +
112G PRO* 3.3 2.3 - - - +
113G VAL* 2.8 39.3 + - + +
115G LEU* 4.0 18.6 - - + -
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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