Contacts of the strand formed by residues 369 - 373 (chain A) in PDB entry 1D1T
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 ARG 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE 3.5 22.5 + - - +
46A CYS* 3.3 30.3 - - - +
47A ARG 4.4 0.4 - - - +
68A GLU* 2.8 42.5 + - - -
171A LEU* 3.6 25.4 - - + +
175A GLY* 3.6 18.9 - - - -
202A GLY* 4.2 21.0 - - - +
203A VAL* 4.4 1.4 - - - +
345A LEU* 2.8 21.0 + - + +
346A ILE* 3.4 7.1 - - + +
347A THR* 2.9 27.6 + - - -
348A HIS 3.6 1.7 + - - +
362A LEU* 5.4 2.0 - - - +
368A ILE* 1.3 86.0 + - + +
370A THR* 1.3 63.2 + - - +
371A VAL* 4.1 0.7 - - + -
1377A NAD 3.2 23.8 + - - -
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Residues in contact with THR 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY* 3.5 2.3 - - - -
45A ILE* 3.0 46.3 + - + +
348A HIS* 3.4 25.1 + - + +
350A LEU* 4.4 10.8 - - + -
358A GLY* 3.9 27.5 + - - -
361A LEU* 4.8 1.3 - - + +
362A LEU* 5.7 0.6 - - - +
367A SER* 3.6 24.6 + - - -
368A ILE 3.8 1.7 + - - -
369A ARG* 1.3 76.5 + - - +
371A VAL* 1.3 71.8 + - - +
372A LEU* 4.9 1.8 - - + -
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Residues in contact with VAL 371 (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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42A ALA* 4.0 16.6 - - + -
43A THR 3.6 7.6 - - - +
44A GLY* 4.8 3.1 - - - -
167A GLU* 3.6 32.8 - - + +
170A CYS* 4.2 13.2 - - - -
171A LEU* 4.8 5.6 - - + -
346A ILE* 3.9 26.5 - - + -
348A HIS 2.9 10.2 + - - +
349A VAL* 3.4 9.7 - - + +
350A LEU* 2.8 27.9 + - - -
370A THR* 1.3 78.3 - - - +
372A LEU* 1.3 76.4 + - - +
373A THR* 4.8 0.9 - - - +
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Residues in contact with LEU 372 (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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42A ALA* 3.4 4.2 - - - -
43A THR* 2.8 40.5 + - + +
45A ILE* 3.9 26.2 - - + -
146A PHE* 4.5 8.7 - - + -
350A LEU* 3.2 13.0 - - + +
351A PRO 4.1 12.3 - - - +
352A PHE* 4.0 22.0 - - + -
354A LYS 4.4 1.1 - - - +
355A ILE* 3.6 57.0 - - + +
358A GLY* 5.4 0.2 - - - -
370A THR* 4.9 2.9 - - + -
371A VAL* 1.3 80.6 - - - +
373A THR* 1.3 60.0 + - - +
374A PHE* 4.6 1.5 - - - -
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Residues in contact with THR 373 (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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41A LEU 3.5 10.5 + - - -
42A ALA* 4.5 5.9 - - - +
167A GLU* 5.5 4.4 - - - +
349A VAL* 4.7 17.0 - - + -
350A LEU 2.7 23.7 + - - +
351A PRO* 3.7 11.0 - - + +
352A PHE* 2.7 32.2 + - - +
371A VAL* 5.3 1.3 - - - -
372A LEU* 1.3 74.3 - - - +
374A PHE* 1.3 77.3 + - - +
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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