Contacts of the strand formed by residues 113 - 120 (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 113 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G CYS 3.8 0.2 - - - +
22G GLU* 3.4 2.1 - - - -
23G LEU* 2.8 39.5 + - + +
49G ILE* 3.7 29.4 - - + -
50G CYS 3.5 10.8 - - - +
51G LEU* 3.8 9.0 - - + -
60G HIS* 3.4 35.2 - - + -
62G VAL* 4.1 12.1 - - + -
83G LEU* 4.7 2.2 - - + -
106G LEU* 3.8 19.3 - - + -
111G GLY* 4.1 2.5 - - - -
112G PRO* 1.3 75.4 - - - +
114G PHE* 1.3 65.4 + - - +
115G LEU* 4.1 4.6 - - + +
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Residues in contact with PHE 114 (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 3.3 7.6 - - - +
22G GLU* 3.3 46.9 - - + -
48G THR 4.6 0.2 - - - -
49G ILE* 3.3 6.8 - - - +
50G CYS* 2.8 41.7 + - + +
52G GLY* 3.8 26.2 - - - -
112G PRO* 4.1 10.5 - - + -
113G VAL* 1.3 72.4 - - - +
115G LEU* 1.3 70.0 + - - +
61H ARG* 3.5 28.5 - - - -
77H PRO 5.8 2.9 - - - -
79H THR* 3.5 46.2 - - + +
107H ARG* 6.0 0.2 - - - -
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Residues in contact with LEU 115 (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* 3.9 17.0 - - + -
20G GLY* 3.1 5.4 - - - -
21G CYS* 2.8 43.1 + - - +
23G LEU* 4.0 23.6 - - + -
46G LEU* 4.0 10.5 - - + -
48G THR 3.5 6.5 - - - -
49G ILE* 3.7 36.6 - - + -
62G VAL* 4.6 4.7 - - + -
104G PHE* 3.9 27.8 - - + -
113G VAL* 4.1 9.9 - - + +
114G PHE* 1.3 84.7 - - - +
116G SER* 1.3 60.3 + - - +
78H VAL* 4.4 2.1 - - - +
79H THR 4.5 4.0 + - - +
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Residues in contact with SER 116 (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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18G LEU* 5.9 0.9 - - - -
19G TRP* 3.5 11.2 - - - -
46G LEU* 3.5 8.0 - - - +
47G HIS* 2.9 26.5 + - - +
48G THR* 2.6 38.4 + - - +
115G LEU* 1.3 73.6 - - - +
117G GLY* 1.3 60.2 + - - +
78H VAL* 3.5 14.8 - - - -
79H THR 3.3 20.4 - - - -
80H ILE* 4.2 10.3 - - - +
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Residues in contact with GLY 117 (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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18G LEU* 3.4 7.3 - - - +
19G TRP* 2.8 36.7 + - - +
45G LEU 2.9 14.8 - - - -
46G LEU* 4.4 0.2 - - - -
47G HIS* 3.7 12.1 - - - -
116G SER* 1.3 78.0 - - - +
118G GLN* 1.3 68.9 + - - +
78H VAL* 4.8 0.2 - - - +
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Residues in contact with GLN 118 (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* 3.6 32.5 - - - +
17G VAL 3.3 10.5 - - - +
18G LEU* 3.9 14.6 - - + +
19G TRP 4.3 0.2 - - - +
44G LEU* 3.6 4.7 - - - +
45G LEU* 2.8 55.3 + - + +
47G HIS* 2.8 29.1 + - + -
117G GLY* 1.3 78.1 - - - +
119G GLU* 1.3 62.9 + - - +
43H ARG* 4.0 0.6 - - - +
97H GLN 2.9 33.6 + - - +
98H LEU* 3.9 15.3 - - - +
99H SER 4.9 0.2 - - - +
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Residues in contact with GLU 119 (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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15G THR 3.8 0.9 - - - +
16G THR* 3.3 4.0 + - - -
17G VAL* 2.7 57.9 + - + +
18G LEU 4.8 2.1 - - - +
19G TRP* 3.8 31.2 - - + +
32G PHE* 3.7 33.6 - - + -
34G PRO* 5.1 5.8 - - - +
42G CYS* 4.5 8.5 - - - -
43G ARG 3.5 6.3 - - - +
44G LEU* 4.7 1.8 - - + -
118G GLN* 1.3 72.6 - - - +
120G ARG* 1.3 58.8 + - - +
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Residues in contact with ARG 120 (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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15G THR 3.4 22.7 - - - +
16G THR* 3.9 12.3 - - - +
42G CYS* 3.4 16.3 - - - -
43G ARG* 2.8 42.4 + - + +
45G LEU* 3.7 32.5 - - + +
97G GLN* 3.1 33.5 + - - +
118G GLN 3.7 0.4 + - - -
119G GLU* 1.3 75.6 - - - +
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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