Contacts of the strand formed by residues 3 - 8 (chain Z) in PDB entry 5A0Q
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 3 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1Z THR 4.6 0.4 - - - +
2Z THR* 1.3 80.5 - - - +
4Z LEU* 1.3 62.1 + - - +
14Z VAL* 5.6 1.8 - - - -
15Z ALA 3.3 6.7 - - - -
16Z ALA* 3.6 19.3 - - + -
33Z LYS* 3.7 10.8 - - + -
34Z VAL* 5.5 1.3 - - + -
44Z THR* 3.1 27.2 - - + +
45Z MET 3.4 24.5 + - - +
46Z ALA* 4.1 2.8 - - - +
100Z MET* 2.8 23.5 - - - +
128Z VAL* 3.0 29.1 + - - +
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Residues in contact with LEU 4 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z THR* 4.4 1.4 - - - +
3Z THR* 1.3 77.6 - - - +
5Z ALA* 1.3 61.9 + - - +
6Z PHE* 3.7 30.3 - - + -
13Z ILE 4.7 1.3 - - - +
14Z VAL* 3.5 5.0 - - - +
15Z ALA* 3.0 35.3 + - + +
126Z PHE 3.5 5.6 - - - +
127Z SER* 3.3 24.0 - - - +
135Z ALA* 4.8 3.1 - - + -
139Z MET* 3.9 7.0 - - + -
156Z ALA* 3.7 24.7 - - + +
159Z ALA* 3.4 34.1 - - + +
160Z ILE* 3.7 24.9 - - + +
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Residues in contact with ALA 5 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Z THR 3.7 0.6 + - - -
4Z LEU* 1.3 74.4 - - - +
6Z PHE* 1.4 63.9 + - - +
12Z VAL* 5.1 0.7 - - + -
13Z ILE 3.3 11.7 - - - +
14Z VAL* 4.4 11.0 - - + -
100Z MET* 3.5 23.3 - - + -
102Z CYS* 4.4 0.7 - - - -
111Z LEU* 3.5 26.0 - - + +
126Z PHE 2.9 32.5 + - - +
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Residues in contact with PHE 6 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Z LEU* 3.7 21.5 - - + -
5Z ALA* 1.4 74.1 - - - +
7Z LYS* 1.4 59.0 + - - +
8Z PHE* 3.8 15.6 - + - -
12Z VAL* 3.4 2.3 - - - +
13Z ILE* 3.0 38.0 + - + -
111Z LEU* 3.5 4.2 - - - +
124Z ALA 3.2 11.7 - - - +
125Z THR* 4.3 4.5 - - - -
139Z MET* 3.5 31.9 - - + -
143Z TYR* 3.7 24.9 - + + -
147Z LEU* 3.8 24.2 - - + -
152Z ALA* 3.6 22.0 - - + -
155Z LEU* 3.9 19.1 - - + -
156Z ALA* 4.0 13.7 - - + -
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Residues in contact with LYS 7 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Z PHE* 1.4 76.3 - - - +
8Z PHE* 1.3 61.1 + - - +
11Z GLY 3.5 4.0 - - - -
12Z VAL* 3.6 22.2 - - + -
109Z PRO* 3.0 45.7 + - + +
110Z GLY* 4.2 6.8 - - - +
111Z LEU* 4.2 10.9 + - + +
112Z TYR* 6.2 0.8 - - - -
122Z SER* 5.6 2.0 + - - -
123Z GLY 4.0 11.5 + - - -
124Z ALA* 3.1 36.2 + - + +
143Z TYR* 2.4 33.3 + - - -
145Z TYR* 3.8 11.9 - - + +
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Residues in contact with PHE 8 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Z PHE* 3.8 18.6 - + - -
7Z LYS* 1.3 78.2 - - - +
9Z ARG* 1.4 63.3 + - - +
10Z HIS* 3.5 19.5 - - + -
11Z GLY* 2.8 44.5 + - - +
13Z ILE* 3.6 32.8 - - + -
109Z PRO* 4.2 5.7 - - - +
143Z TYR* 4.6 1.1 - - + -
144Z SER 4.1 6.7 - - - +
145Z TYR* 3.6 30.3 + - - +
147Z LEU* 3.7 28.7 - - + -
148Z GLU 4.2 6.1 - - - -
149Z VAL* 4.2 5.4 - - - -
152Z ALA* 3.3 27.1 - - + -
178Z HIS* 4.2 4.0 - - - -
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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