Contacts of the helix formed by residues 318 - 322 (chain B) 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 VAL 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASN* 5.2 1.0 - - - +
309A PHE* 4.0 17.0 - - + +
310A THR* 4.0 34.3 - - + +
311A GLY* 5.6 0.4 - - - -
93B PHE* 4.6 8.3 - - + -
94B LEU* 3.4 30.7 - - + -
109B ASN* 2.8 34.2 + - - +
110B LEU* 3.9 16.2 - - + -
116B ILE* 6.2 0.9 - - + -
317B CYS* 1.3 75.8 - - - +
319B PHE* 1.3 67.8 + - + +
320B GLY 3.1 1.1 - - - -
321B GLY* 2.9 6.1 + - - +
2377B NAD 3.5 6.5 - - - +
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 5.2 4.0 - - + -
93B PHE* 3.6 23.7 - + + -
94B LEU* 3.6 19.7 - - + -
172B ILE 3.3 17.9 - - - -
173B GLY* 3.6 25.1 - - - -
174B CYS* 3.6 2.2 - - - -
177B SER* 3.6 20.8 - - - +
178B THR* 3.3 24.0 - - - -
318B VAL* 1.3 74.4 - - + +
320B GLY* 1.3 61.5 + - - +
321B GLY 3.1 1.2 + - - -
322B LEU* 3.2 34.7 + - + +
324B SER* 3.8 25.1 - - - -
328B VAL* 3.9 19.5 - - + -
2377B NAD 2.9 14.1 + - - -
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B SER 3.9 2.0 - - - -
178B THR* 3.1 30.9 - - - +
181B GLY* 3.2 23.2 - - - +
182B ALA 3.5 3.4 - - - -
185B LYS* 3.6 7.3 - - - +
186B THR* 3.6 6.9 + - - -
317B CYS* 3.4 14.3 - - - -
318B VAL 3.1 2.0 + - - -
319B PHE* 1.3 76.2 - - - +
321B GLY* 1.3 60.3 + - - +
322B LEU* 3.2 2.5 + - - +
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Residues in contact with GLY 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP 5.4 2.6 - - - +
108B GLY 5.0 1.7 - - - +
109B ASN* 3.3 23.7 - - - +
185B LYS* 4.4 12.5 - - - +
186B THR* 3.6 13.6 + - - -
317B CYS* 4.0 1.6 - - - -
318B VAL 2.9 10.2 + - - -
320B GLY* 1.3 75.7 - - - +
322B LEU* 1.3 61.2 + - - +
323B LYS* 3.9 2.4 + - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 3.6 6.4 - - - +
109B ASN* 2.8 21.2 + - - +
177B SER* 3.5 36.6 - - - +
180B TYR* 6.0 3.1 - - + -
181B GLY* 4.4 9.0 - - - -
185B LYS* 4.1 18.8 - - + -
319B PHE* 3.2 28.7 + - + +
320B GLY 3.2 9.8 - - - +
321B GLY* 1.3 79.2 - - - +
323B LYS* 1.3 60.6 + - - +
324B SER 3.5 3.3 + - - -
327B ASP* 3.5 28.0 - - + +
328B VAL* 5.5 0.2 - - + -
331B LEU* 3.6 20.9 - - + -
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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