Contacts of the helix formed by residues 318 - 322 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C PHE* 4.9 6.1 - - + -
94C LEU* 3.6 32.3 - - + -
109C ASN* 2.7 39.2 + - - +
110C LEU* 3.9 15.7 - - + -
116C ILE* 6.5 0.2 - - + -
317C CYS* 1.3 81.9 - - - +
319C PHE* 1.3 66.8 + - + +
320C GLY 3.2 0.2 - - - -
321C GLY* 3.2 3.3 + - - +
3377C NAD 3.6 4.3 - - - +
285D ASN* 5.0 1.9 - - - +
309D PHE* 3.7 33.2 - - + +
310D THR* 4.3 13.7 - - + +
311D GLY* 5.8 0.4 - - - -
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Residues in contact with PHE 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 5.1 4.7 - - + -
93C PHE* 3.7 26.5 - + + -
94C LEU* 3.6 31.9 - - + -
172C ILE 3.4 26.9 - - - -
173C GLY* 3.8 17.7 - - - -
174C CYS* 3.9 1.3 - - - -
177C SER* 3.5 16.8 - - - -
178C THR* 3.5 18.8 - - - -
318C VAL* 1.3 74.3 - - + +
320C GLY* 1.3 63.8 + - - +
322C LEU* 2.9 32.0 + - + +
324C SER* 4.0 16.2 - - - -
328C VAL* 3.6 26.0 - - + -
3377C NAD 2.8 14.8 + - - -
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Residues in contact with GLY 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C SER 3.6 4.5 - - - -
178C THR* 3.2 29.7 - - - +
181C GLY* 2.9 29.6 - - - +
182C ALA 3.5 4.3 - - - -
185C LYS* 3.7 4.5 - - - +
186C THR* 3.7 4.3 - - - -
317C CYS* 3.3 13.6 - - - -
318C VAL 3.2 1.2 - - - -
319C PHE* 1.3 75.8 - - - +
321C GLY* 1.3 59.7 + - - +
322C LEU* 3.2 2.0 + - - +
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Residues in contact with GLY 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ASN* 3.3 22.2 + - - +
185C LYS* 4.4 14.5 - - - +
186C THR* 3.7 13.4 + - - -
317C CYS* 3.8 2.6 - - - -
318C VAL 3.2 6.7 + - - -
319C PHE 2.9 2.2 + - - -
320C GLY* 1.3 75.8 - - - +
322C LEU* 1.3 63.2 + - - +
323C LYS* 3.9 2.9 + - - +
327C ASP* 4.8 0.2 - - - +
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Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LEU* 3.5 6.8 - - - +
109C ASN* 2.9 23.4 + - - +
177C SER* 3.6 24.0 - - - +
180C TYR* 6.1 2.5 - - + -
181C GLY* 4.7 6.1 - - - -
185C LYS* 3.5 21.8 - - + +
319C PHE* 2.9 33.5 + - + +
320C GLY 4.2 5.2 - - - +
321C GLY* 1.3 79.6 - - - +
323C LYS* 1.3 60.5 + - - +
324C SER 3.4 4.1 + - - +
327C ASP* 3.3 28.0 - - + +
328C VAL* 4.8 2.5 - - + -
331C LEU* 3.3 33.7 - - + -
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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