Contacts of the strand formed by residues 101 - 106 (chain D) in PDB entry 3TQS
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 LEU 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D THR* 3.6 32.1 - - + +
37D VAL* 3.9 24.2 - - + -
92D PHE* 3.4 40.8 - - + +
95D VAL* 3.9 17.5 - - + +
97D THR* 3.9 19.5 - - + -
99D LYS 4.5 1.1 - - - +
100D PRO* 1.3 73.6 - - - +
102D ARG* 1.3 63.1 + - - +
103D VAL* 3.7 8.2 + - + -
125D CYS* 2.7 20.9 + - + +
126D ILE* 3.5 7.6 - - + +
127D GLU 2.8 25.0 + - - -
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Residues in contact with ARG 102 (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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27D ALA 5.1 0.2 + - - -
28D ILE* 2.7 45.0 + - + +
29D HIS 3.3 10.3 + - - -
30D PRO* 3.8 0.2 - - - +
34D ASP* 2.9 40.7 + - + -
35D THR 2.9 18.3 + - - +
36D LEU* 3.2 18.5 - - + +
37D VAL 3.0 21.2 + - - +
100D PRO 4.9 1.1 - - - +
101D LEU* 1.3 73.2 - - - +
103D VAL* 1.3 62.1 + - - +
104D VAL* 4.7 3.1 - - + -
127D GLU* 3.4 28.7 + - - +
128D ASP* 2.9 42.6 + - - +
130D HIS* 3.7 9.5 - - - -
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 3.4 20.9 - - + +
39D ILE* 4.2 13.0 - - + -
92D PHE* 4.7 8.1 - - + -
101D LEU* 4.4 7.0 - - + +
102D ARG* 1.3 72.3 - - - +
104D VAL* 1.3 73.2 + - - +
119D LEU* 4.5 17.0 - - + -
126D ILE* 4.2 27.8 - - + -
128D ASP* 3.0 6.7 + - - +
129D MSE 3.2 15.5 - - + -
130D HIS* 3.0 22.9 + - - -
131D PHE* 3.6 24.2 - - + -
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Residues in contact with VAL 104 (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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24D ILE* 6.3 0.2 - - + -
28D ILE* 3.7 34.5 - - + -
36D LEU* 4.4 12.8 - - + -
37D VAL 2.8 11.3 + - - +
38D GLU* 3.2 27.1 - - + -
39D ILE* 2.9 23.4 + - - +
46D LEU* 4.6 5.8 - - + -
50D LEU* 4.2 18.2 - - + -
102D ARG* 4.4 7.9 - - + +
103D VAL* 1.3 81.3 - - - +
105D GLY* 1.3 60.0 + - - +
130D HIS* 3.1 17.5 - - + +
131D PHE* 3.7 9.6 - - - -
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Residues in contact with GLY 105 (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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38D GLU* 4.5 5.2 - - - -
39D ILE* 3.0 14.1 - - - -
40D GLY 5.2 0.2 - - - -
46D LEU* 5.5 4.9 - - - +
104D VAL* 1.3 80.5 - - - +
106D ASN* 1.3 55.0 + - - -
130D HIS 3.2 6.5 + - - +
131D PHE* 3.3 15.1 - - - -
132D MSE 2.8 32.1 + - - +
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Residues in contact with ASN 106 (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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13D HIS* 3.0 28.3 + - - +
14D PHE* 5.1 0.2 - - - +
15D LEU* 4.9 6.4 - - - +
39D ILE 3.0 6.9 + - - -
40D GLY* 3.7 28.6 + - - +
105D GLY* 1.3 72.7 - - - +
107D LEU* 1.3 70.8 + - - +
108D PRO* 4.0 5.0 - - - +
132D MSE 3.6 29.5 - - + +
174D PHE* 4.4 10.1 - - - -
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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