Contacts of the strand formed by residues 100 - 105 (chain A) in PDB entry 1TOG
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 ALA 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLN* 3.3 34.3 + - - +
88A PHE* 4.0 22.9 - - + -
94A LEU* 3.9 9.1 + - + +
98A LYS* 3.5 4.4 - - - -
99A ARG* 1.3 81.4 + - - +
101A ARG* 1.3 71.6 + - - +
271A THR* 4.1 4.0 - - + -
272A LEU 3.1 9.2 - - - +
273A VAL* 4.1 5.8 - - + -
280A VAL* 4.8 0.2 - - - -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASP* 4.0 8.3 + - - -
84A GLN* 3.9 0.9 - - - -
98A LYS 5.8 1.1 - - - -
100A ALA* 1.3 82.0 - - - +
102A THR* 1.3 62.4 + - - +
270A CYS 3.8 1.6 - - - +
271A THR* 3.4 2.0 - - - -
272A LEU* 2.9 34.2 + - + +
280A VAL* 4.0 16.4 - - + -
281A ASP* 2.7 52.3 + - - +
284A PHE* 3.4 55.3 - - + +
288A LYS* 4.2 11.5 - - - +
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASP* 4.0 11.4 - - - +
79A PHE* 5.2 1.1 - - + -
80A GLY* 4.1 27.8 - - - -
83A THR* 4.2 6.7 - - + -
84A GLN* 2.8 32.3 + - - +
101A ARG* 1.3 75.0 - - - +
103A ALA* 1.3 65.2 + - - +
104A GLN 4.2 1.1 + - - +
269A ALA* 3.8 24.9 - - + -
270A CYS 3.6 3.4 - - - +
271A THR* 2.9 23.2 + - - +
284A PHE* 3.6 10.6 - - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASP* 3.7 12.1 - - + -
102A THR* 1.3 74.4 - - - +
104A GLN* 1.3 64.2 + - - +
105A THR* 3.5 4.7 - - + +
269A ALA* 3.2 2.9 - - - -
270A CYS* 2.8 43.2 + - + +
284A PHE* 3.8 18.7 - - + -
287A MET* 4.8 2.2 - - - -
291A ILE* 3.8 29.2 - - + -
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.6 4.3 - - - +
73A ILE 4.5 2.6 - - - +
74A ASP 3.0 16.5 + - - +
75A GLY* 3.3 3.2 - - - -
76A ILE* 2.9 34.1 + - - +
79A PHE* 3.6 27.2 - - + -
80A GLY* 6.2 0.2 - - - -
102A THR* 4.1 2.4 - - - +
103A ALA* 1.3 74.4 - - - +
105A THR* 1.3 65.0 + - - +
266A ARG 5.8 0.6 + - - -
267A VAL* 6.2 0.2 - - - -
268A GLY 3.6 7.4 - - - +
295A TYR* 4.0 3.8 + - - -
298A PRO* 3.3 32.7 - - + +
299A PRO* 2.8 35.0 + - - +
303A ALA* 3.2 21.2 - - + +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA* 3.5 16.2 - - + +
104A GLN* 1.3 81.2 + - - +
106A PRO* 1.3 70.9 - - - +
107A GLY 2.8 28.2 + - - -
110A GLY 4.0 0.4 - - - -
111A ALA* 3.3 24.2 - - - +
114A VAL* 4.3 8.3 - - + -
266A ARG 3.4 4.5 - - - +
267A VAL* 4.0 0.3 - - - -
268A GLY 2.9 18.6 + - - +
269A ALA 3.2 13.7 + - - -
270A CYS* 3.9 14.1 - - + +
291A ILE* 5.2 0.2 - - + -
295A TYR* 3.6 12.6 - - - +
298A PRO* 4.5 4.7 - - - -
299A PRO* 5.0 0.4 - - - +
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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