Contacts of the strand formed by residues 303 - 306 (chain C) in PDB entry 1TYG
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 GLY 303 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C LEU* 4.9 1.6 - - - -
114C ARG* 3.0 14.6 - - - -
116C LEU* 4.9 0.2 - - - -
281C VAL 3.5 3.1 + - - +
282C ILE* 3.2 33.2 - - - -
283C VAL 3.2 5.4 + - - -
297C MET* 3.5 8.2 - - - +
301C ALA* 3.3 6.1 - - - +
302C ASP* 1.3 83.6 - - - +
304C VAL* 1.3 66.4 + - - +
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Residues in contact with VAL 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ARG 3.0 6.1 + - - -
115C LEU* 3.7 5.9 - - - +
116C LEU 2.8 27.2 + - - +
282C ILE* 3.8 2.4 - - - +
283C VAL* 3.4 8.3 - - + +
287C ILE* 3.7 18.6 - - + -
293C ALA* 3.7 24.9 - - - +
296C ALA* 3.7 18.4 - - + -
297C MET* 3.9 8.4 - - - -
303C GLY* 1.3 77.9 - - - +
305C LEU* 1.3 66.4 + - - +
306C LEU* 3.3 31.0 - - + -
327C VAL* 4.4 11.2 - - + +
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.2 39.7 - - + +
117C LEU 4.1 5.6 - - - +
118C GLY* 4.3 2.2 - - - +
141C THR* 3.3 29.4 - - + -
169C LEU* 4.4 2.5 - - + -
198C LYS* 3.7 32.3 - - + +
252C MET* 3.6 21.3 - - + -
282C ILE* 3.5 7.4 - - + +
283C VAL 2.8 7.2 + - - +
284C ASP* 3.3 35.2 - - + +
287C ILE* 4.8 1.2 - - - +
304C VAL* 1.3 74.7 - - - +
306C LEU* 1.3 69.8 + - - +
2400C PO4 4.2 2.5 + - - +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.2 20.2 - - + -
116C LEU 3.1 5.5 + - - -
117C LEU* 3.5 8.6 - - + +
118C GLY 3.3 17.3 + - - -
287C ILE* 4.0 24.9 - - + -
293C ALA* 4.4 3.4 - - + -
304C VAL* 3.3 26.5 - - + -
305C LEU* 1.3 77.4 - - - +
307C ASN* 1.3 61.8 + - - +
309C ALA* 4.8 4.9 - - + +
310C VAL* 3.4 30.5 - - + -
323C MET* 3.7 28.5 - - + -
327C VAL* 5.3 0.4 - - + -
2400C PO4 3.7 14.1 - - - +
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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
------------------------------------------------------------
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