Contacts of the strand formed by residues 268 - 272 (chain A) in PDB entry 4TZ1
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 PHE 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLY 3.8 10.3 - - - -
126A LEU* 3.6 12.1 - - + -
157A GLU* 3.7 28.5 - - - +
158A ASN* 3.7 24.9 - - + -
180A ARG* 3.3 36.3 - - - -
265A GLU* 6.3 0.4 - - + -
266A LYS* 3.5 15.7 - - - +
267A PRO* 1.3 75.6 - - - +
269A LEU* 1.3 75.1 + - - +
270A TYR* 3.8 4.7 + - + -
278A VAL* 3.3 7.1 - - - +
279A PHE* 2.9 65.0 + + + -
281A PRO* 4.5 3.6 - - + -
352A LEU* 4.4 4.3 - - - -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.8 27.1 - - + -
68A VAL* 5.7 0.2 - - + -
102A MET* 4.1 27.0 - - + +
123A GLY 4.0 6.9 - - - +
124A LEU* 3.8 19.2 - - + +
268A PHE* 1.3 83.9 - - - +
270A TYR* 1.3 65.0 + - - +
276A TYR* 3.9 37.2 - - + -
277A LYS 3.2 24.2 - - - +
278A VAL* 4.1 12.1 - - + -
304A LEU* 4.2 13.5 - - + -
330A LEU* 4.8 3.6 - - + -
352A LEU* 4.1 11.7 - - + +
354A LEU* 4.8 6.9 - - + +
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.3 11.4 - - - +
125A GLY 3.1 30.5 - - - +
126A LEU* 3.4 36.5 - - + +
268A PHE* 4.1 2.7 - + + -
269A LEU* 1.3 77.2 - - - +
271A LEU* 1.3 77.2 + - - +
272A ASP* 3.4 26.6 + - - -
275A ASP 3.6 0.2 - - - +
276A TYR* 3.9 3.3 - - - -
277A LYS* 3.0 50.9 + - + +
279A PHE* 3.6 36.3 - - + -
301A SER* 2.6 26.7 + - - -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 3.5 46.9 - - + +
105A PRO* 3.8 21.3 - - + +
124A LEU* 2.8 29.3 + - + +
125A GLY* 5.3 1.4 - - - -
270A TYR* 1.3 87.9 - - - +
272A ASP* 1.3 56.7 + - - +
273A GLY 2.8 25.6 + - - +
274A ASP* 3.4 23.8 - - + -
275A ASP 3.7 5.8 - - - +
276A TYR* 4.6 19.7 - - + +
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A TYR* 3.4 32.2 + - - -
271A LEU* 1.3 69.8 - - - +
273A GLY* 1.3 52.8 - - - +
274A ASP 2.2 21.0 + - - -
275A ASP* 2.5 34.2 + - + +
277A LYS* 3.9 27.0 + - + +
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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