Contacts of the strand formed by residues 279 - 285 (chain I) in PDB entry 1DZG
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 ILE 279 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138I SER* 4.9 13.9 - - - +
140I LEU* 4.4 25.4 - - + -
221I PHE* 3.5 44.2 - - + -
274I PHE* 3.2 31.3 + - + +
277I ASP 4.7 0.4 - - - +
278I ASP* 1.3 93.4 + - - +
280I THR* 1.3 62.8 + - - +
412I ILE* 3.9 18.4 - - + -
413I ARG 3.3 5.4 - - - +
414I GLU* 3.7 23.3 - - + -
421I ILE* 4.4 4.0 - - + -
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Residues in contact with THR 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I GLU* 2.8 37.9 + - - +
272I LEU 4.0 2.0 - - - -
273I PRO* 3.6 29.2 - - + -
274I PHE* 3.8 8.7 - - - -
277I ASP 4.5 5.6 - - - +
278I ASP 4.4 0.2 + - - -
279I ILE* 1.3 75.7 - - - +
281I MET* 1.3 62.1 + - - +
282I VAL* 4.1 2.1 - - - +
412I ILE* 3.3 9.5 - - - +
413I ARG* 3.0 43.1 + - - +
415I VAL* 3.8 15.4 - - + +
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Residues in contact with MET 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I TRP* 3.8 27.1 - - + -
270I LEU 3.8 1.2 - - - +
272I LEU* 2.9 40.4 + - + +
274I PHE* 3.9 14.1 - - + -
280I THR* 1.3 77.0 - - - +
282I VAL* 1.3 62.3 + - - +
283I LEU* 3.5 28.4 + - + +
320I MET* 4.1 9.2 - - - -
323I PHE* 3.4 34.5 - - + -
373I LEU* 5.1 0.7 - - - -
375I VAL* 4.5 8.5 - - + -
380I CYS* 6.1 0.2 - - - -
410I VAL* 3.7 15.0 - - + -
411I PHE 3.2 8.1 - - - +
412I ILE* 4.4 11.7 - - + -
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Residues in contact with VAL 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I VAL* 3.6 25.8 - - + -
270I LEU 3.4 12.6 - - - +
271I GLU* 4.0 16.4 - - + +
281I MET* 1.3 75.7 - - - +
283I LEU* 1.3 65.1 + - - +
284I ILE* 4.4 8.5 - - + -
304I LEU* 6.5 0.2 - - + -
308I LEU* 4.1 15.0 - - + -
311I LEU* 5.2 0.2 - - + -
410I VAL* 3.4 5.0 - - - -
411I PHE* 2.8 49.8 + - + +
413I ARG* 3.6 34.8 - - + -
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Residues in contact with LEU 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I GLN 3.6 1.0 - - - +
269I VAL* 3.3 6.9 - - - +
270I LEU* 2.9 43.4 + - + +
272I LEU* 4.4 3.8 - - + -
281I MET* 3.5 34.8 - - + +
282I VAL* 1.3 81.1 - - - +
284I ILE* 1.3 64.2 + - - +
285I LEU 4.0 0.2 - - - -
320I MET* 3.7 27.8 - - + -
402I PHE* 3.8 34.0 - - + -
404I ALA* 5.4 0.9 - - + -
408I PHE* 3.9 26.9 - - + -
409I LEU 3.5 5.8 - - - +
410I VAL* 4.5 3.4 - - + -
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Residues in contact with ILE 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267I THR* 3.6 21.1 - - + -
268I GLN 3.7 1.8 - - - -
269I VAL* 3.8 23.8 - - + -
282I VAL* 4.4 5.2 - - + -
283I LEU* 1.3 80.1 - - - +
285I LEU* 1.3 58.1 + - - +
286I PRO* 3.7 3.7 - - + +
292I LEU* 4.6 1.7 - - + +
295I VAL* 4.2 10.8 - - + -
304I LEU* 4.7 3.4 - - + -
307I TRP* 3.5 34.5 - - + -
408I PHE* 3.1 8.3 - - - +
409I LEU* 3.0 52.1 + - + -
411I PHE* 3.7 24.9 - - + -
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Residues in contact with LEU 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266I GLY 4.0 0.7 - - - +
267I THR* 3.5 2.2 - - - -
268I GLN* 2.8 63.3 + - - +
283I LEU 4.0 0.4 - - - -
284I ILE* 1.3 73.9 - - - +
286I PRO* 1.3 68.9 - - + +
402I PHE* 3.8 25.4 - - + -
403I LYS 3.2 28.9 - - - +
404I ALA* 4.1 12.8 - - + -
406I ARG* 3.4 43.7 - - + +
407I PRO 4.0 4.3 - - - +
408I PHE* 3.9 11.4 - - + -
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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
------------------------------------------------------------
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