Contacts of the strand formed by residues 45 - 49 (chain P) in PDB entry 2AAZ
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 45 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O ARG* 4.0 10.9 + - - +
36P VAL* 3.4 4.5 - - - +
37P ARG* 2.8 43.0 + - - +
38P PRO 5.2 0.2 + - - -
39P ASP* 4.2 6.7 - - - +
44P GLY* 1.3 81.7 - - - +
46P VAL* 1.3 59.7 + - - +
47P ALA* 4.4 4.5 - - - +
255P ASP* 5.5 0.2 + - - -
257P HIS* 3.8 30.4 - - + +
258P VAL 3.5 11.2 - - - -
259P TYR* 3.6 29.6 - - + -
260P ARG* 3.7 12.3 - - - +
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Residues in contact with VAL 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P ILE* 3.0 41.9 - - + +
31P ILE* 4.6 11.2 - - - +
34P GLY 3.4 22.9 - - - +
35P GLU 3.2 6.3 - - - +
36P VAL* 4.6 9.0 - - + +
45P THR* 1.3 75.4 - - - +
47P ALA* 1.3 60.5 + - - +
257P HIS* 3.3 0.7 - - - -
258P VAL* 2.9 41.1 + - + +
260P ARG* 5.4 3.1 - - - -
263P VAL* 5.0 8.3 - - + -
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Residues in contact with ALA 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O PHE* 5.2 4.2 - - + -
30P ILE* 4.1 2.2 - - - -
34P GLY* 3.6 2.7 - - - -
35P GLU* 2.9 41.8 + - - +
37P ARG* 4.2 19.2 - - - +
45P THR* 4.4 2.5 - - - +
46P VAL* 1.3 76.9 - - - +
48P LEU* 1.3 68.5 + - - +
255P ASP* 3.7 13.5 - - - +
256P ALA 3.2 13.9 - - - +
257P HIS* 3.5 13.5 - - + -
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Residues in contact with LEU 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O PHE* 5.0 4.3 - - - -
26P LEU* 4.6 4.0 - - + -
29P ARG* 3.6 52.3 - - + +
30P ILE* 3.9 23.5 - - + +
33P VAL* 4.0 13.0 - - + +
34P GLY* 3.8 17.5 - - - +
35P GLU* 6.0 0.2 - - + -
47P ALA* 1.3 83.6 - - - +
49P PHE* 1.3 60.9 + - - +
51P PRO* 4.6 9.2 - - + -
254P GLY 3.6 0.5 - - - +
255P ASP* 4.0 1.0 - - - -
256P ALA* 3.0 35.0 + - + +
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Residues in contact with PHE 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55O ARG* 4.0 8.5 + - - -
192O GLN* 3.5 36.8 - - + -
194O PHE* 3.3 59.2 - + + -
210O SER* 3.9 22.7 - - - -
211O CYS 4.3 2.0 - - - -
212O LEU* 3.8 28.5 - - + -
248O GLU* 5.5 0.4 - - - +
250O ILE* 4.4 4.7 - - + -
48P LEU* 1.3 75.7 - - - +
50P ALA* 1.3 74.7 + - + +
51P PRO* 3.4 1.6 - - - +
254P GLY* 3.2 32.3 - - - -
255P ASP 4.0 0.4 - - - -
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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
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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