Contacts of the strand formed by residues 102 - 108 (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 102 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F LEU* 6.1 0.9 - - + -
30G TRP 3.9 0.7 - - - +
31G THR* 3.1 1.5 - - - -
32G PHE* 2.6 63.6 + - + +
44G LEU* 4.2 13.0 - - + -
64G ILE* 4.6 15.5 - - + -
67G PRO* 6.0 2.9 - - + -
98G LEU* 3.9 32.1 - - + -
99G SER 3.3 22.0 - - - +
100G PRO* 4.4 1.1 - - + -
101G PRO* 1.3 75.0 - - - +
103G THR* 1.3 61.7 + - - +
104G PHE* 4.1 8.4 + - + -
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Residues in contact with THR 103 (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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29G THR* 4.6 6.1 - - - -
30G TRP 3.3 8.5 - - - +
31G THR* 3.0 33.0 + - + +
64G ILE* 3.3 9.3 - - - +
65G LEU* 3.0 59.5 + - + +
101G PRO* 5.4 2.3 - - - +
102G VAL* 1.3 74.6 + - - +
104G PHE* 1.3 69.4 + - - +
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Residues in contact with PHE 104 (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* 3.7 33.2 - + - -
21G CYS* 5.0 3.8 - - - -
23G LEU* 4.2 20.5 - - + +
29G THR* 3.1 6.4 - - - -
30G TRP* 2.7 42.8 + - + +
32G PHE* 5.0 1.8 - - + -
44G LEU* 3.9 14.8 - - + -
46G LEU* 4.0 13.5 - - + -
62G VAL* 4.5 2.5 - - + -
63G GLU 3.4 4.0 - - - +
64G ILE* 3.8 23.6 - - + -
80G ILE* 3.8 24.7 - - + -
98G LEU* 3.8 20.6 - - + -
102G VAL* 4.5 13.2 - - + -
103G THR* 1.3 75.1 - - - +
105G GLN* 1.3 61.4 + - - +
115G LEU* 3.9 14.1 - - + -
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Residues in contact with GLN 105 (chain G).
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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23G LEU* 4.4 4.3 - - - -
28G ARG* 3.1 13.8 + - - +
29G THR* 3.1 31.6 - - + +
62G VAL* 3.5 2.4 - - - +
63G GLU* 2.8 45.0 + - - +
65G LEU* 3.9 35.9 - - + +
104G PHE* 1.3 77.1 - - - +
106G LEU* 1.3 70.0 + - - +
107G ARG* 2.9 36.4 + - - +
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Residues in contact with LEU 106 (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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23G LEU* 3.9 21.4 - - + +
24G SER* 3.6 36.1 - - - +
28G ARG* 2.7 62.0 + - - +
60G HIS* 4.1 3.1 - - + -
61G ARG 3.6 11.9 - - - +
62G VAL* 4.3 7.4 - - + +
105G GLN* 1.3 69.8 - - - +
107G ARG* 1.3 56.9 + - - +
108G ALA 3.1 23.3 - - - +
109G GLY 3.5 15.5 - - - +
111G GLY 4.1 8.5 - - - +
113G VAL* 3.8 22.9 - - + -
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Residues in contact with ARG 107 (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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53F GLU* 5.6 0.2 - - - -
28G ARG* 4.3 4.4 + - - -
61G ARG* 2.8 38.5 + - - +
63G GLU* 3.0 52.0 + - + +
77G PRO* 5.1 6.9 - - - +
105G GLN* 2.9 33.3 + - - +
106G LEU* 1.3 75.4 + - - +
108G ALA* 1.3 59.3 + - - +
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Residues in contact with ALA 108 (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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53F GLU* 3.6 39.7 - - + +
28G ARG* 4.6 0.9 - - - +
59G MET 4.0 7.4 - - - +
60G HIS* 3.2 1.6 - - - -
61G ARG* 2.9 30.3 + - + +
106G LEU* 3.1 12.5 - - - +
107G ARG* 1.3 79.8 - - - +
109G GLY* 1.3 62.5 + - - +
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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