Contacts of the strand formed by residues 267 - 273 (chain L) 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 THR 267 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261L ARG 3.6 0.5 - - - +
262L ARG* 3.3 3.8 - - - -
263L VAL* 2.9 34.8 + - + +
264L ALA 3.6 15.3 + - - -
265L GLU 4.1 1.6 + - - -
266L GLY* 1.3 76.7 - - - +
268L GLN* 1.3 69.7 + - - +
269L VAL* 4.6 8.5 - - + -
284L ILE* 4.2 17.7 - - + -
285L LEU 3.7 9.9 - - - +
286L PRO* 3.9 17.0 - - + +
290L LYS* 4.1 13.0 + - - -
295L VAL* 4.6 12.9 - - + +
307L TRP* 4.8 7.6 - - + -
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Residues in contact with GLN 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I GLU* 4.7 1.6 + - - -
388I VAL 3.1 25.1 + - - -
389I VAL* 3.8 13.2 - - + +
390I ILE 5.1 0.9 + - - +
260L TYR* 2.9 39.1 + - + +
261L ARG 3.5 3.1 - - - -
262L ARG* 4.0 12.3 - - + +
266L GLY 4.8 3.1 - - - +
267L THR* 1.3 76.2 - - - +
269L VAL* 1.3 62.2 + - - +
270L LEU 4.0 0.8 + - - -
283L LEU 3.9 0.3 - - - +
284L ILE* 3.4 5.2 - - - +
285L LEU* 2.6 60.9 + - + +
286L PRO 5.2 4.0 - - - +
287L LYS* 5.9 1.0 - - - -
288L PRO* 5.9 2.8 - - - +
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Residues in contact with VAL 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260L TYR* 3.5 5.9 - - - -
261L ARG 2.9 31.5 + - - +
263L VAL* 3.5 28.0 - - + -
267L THR* 4.6 3.6 - - + -
268L GLN* 1.3 74.8 - - - +
270L LEU* 1.3 58.6 + - - +
282L VAL* 4.2 13.9 - - + -
283L LEU 3.5 9.6 - - - +
284L ILE* 3.8 19.3 - - + -
307L TRP* 4.1 25.8 - - + +
308L LEU* 5.4 3.1 - - + +
311L LEU* 3.7 25.9 - - + +
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Residues in contact with LEU 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389I VAL* 4.0 27.8 - - + -
258L PHE* 3.8 26.9 - - + -
259L ARG 3.8 4.5 - - - +
260L TYR* 4.4 9.6 - - + -
268L GLN 4.0 1.6 - - - -
269L VAL* 1.3 76.8 - - - +
271L GLU* 1.3 66.9 + - - +
272L LEU* 3.5 34.6 + - + -
282L VAL* 3.4 2.0 - - - -
283L LEU* 2.7 54.5 + - + +
285L LEU* 5.9 0.8 - - + +
316L LEU* 4.5 11.7 - - + -
318L VAL* 3.8 20.9 - - + -
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Residues in contact with GLU 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L PHE* 3.5 12.8 - - - -
259L ARG* 3.0 61.4 + - + +
270L LEU* 1.3 73.7 - - - +
272L LEU* 1.3 65.1 + - - +
273L PRO* 3.2 12.5 - - + +
280L THR* 2.6 40.5 + - + +
281L MET 3.4 9.6 - - - +
282L VAL* 3.5 12.7 - - + +
308L LEU* 4.9 0.4 - - - -
311L LEU* 4.1 12.1 - - + -
413L ARG* 2.6 19.2 + - - -
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Residues in contact with LEU 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L TRP* 3.4 34.3 - - + -
229L PHE* 4.8 9.2 - - + -
258L PHE* 3.5 26.5 - - + -
270L LEU* 3.5 32.3 - - + +
271L GLU* 1.3 70.5 - - - +
273L PRO* 1.3 69.2 - - - +
274L PHE* 4.3 0.2 - - - -
281L MET* 2.9 36.7 + - + +
283L LEU* 4.3 12.8 - - + -
318L VAL* 4.4 8.1 - - + -
320L MET* 3.6 31.6 - - - -
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Residues in contact with PRO 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L TRP* 3.9 6.4 - - - -
226L LYS* 3.1 49.7 + - + +
227L SER 6.3 0.2 - - - +
258L PHE* 4.3 13.2 - - + -
259L ARG 6.1 0.2 - - - +
271L GLU* 3.2 14.8 - - + +
272L LEU* 1.3 87.9 - - - +
274L PHE* 1.3 65.2 + - - +
277L ASP* 4.1 14.4 - - - +
280L THR* 3.5 26.5 - - + -
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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