Contacts of the strand formed by residues 24 - 29 (chain N) in PDB entry 1PP9
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 ARG 24 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16N VAL* 4.7 10.8 - - + -
17N SER 3.5 4.9 - - - +
18N GLN* 3.9 29.4 - - + +
22N GLY 3.5 6.1 + - - +
23N LEU* 1.3 77.5 - - - +
25N VAL* 1.3 62.1 + - - +
26N ALA 4.2 0.4 - - - -
42N ASP* 5.4 1.4 + - - -
193N PRO 3.6 20.6 + - - -
195N MET 3.4 13.6 + - - +
196N VAL* 3.4 20.3 - - + +
197N LEU 2.9 25.3 + - - -
383N LEU* 3.1 41.6 + - + +
384N LEU* 3.9 24.0 - - - +
387N GLY* 4.4 7.5 + - - -
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Residues in contact with VAL 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N VAL* 3.4 1.1 - - - -
17N SER 2.8 39.0 + - - +
19N LEU* 4.3 6.5 - - + -
23N LEU* 4.2 14.8 - - + +
24N ARG* 1.3 79.2 - - - +
26N ALA* 1.3 61.1 + - - +
197N LEU* 3.4 13.9 - - + +
205N HIS* 3.2 9.6 - - + -
208N LEU* 3.6 32.8 - - + -
209N LEU* 4.0 30.7 - - + +
212N ALA* 3.7 21.8 - - + -
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Residues in contact with ALA 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N THR* 4.2 2.2 - - + -
15N GLN 3.0 11.7 - - - +
16N VAL* 3.9 19.1 - - + -
24N ARG 4.2 0.6 - - - -
25N VAL* 1.3 75.4 - - - +
27N SER* 1.3 63.4 + - - +
196N VAL* 4.8 2.9 - - + +
197N LEU 2.9 8.5 + - - +
198N ALA* 3.3 5.4 - - - -
199N ALA 3.1 22.0 + - - -
205N HIS* 4.2 0.4 - - - -
208N LEU* 3.5 3.6 - - - +
379N ILE* 3.5 24.4 - - + +
383N LEU* 4.5 10.1 - - + -
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Residues in contact with SER 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N GLU 4.3 0.5 - - - +
14N THR* 3.4 5.3 - - - +
15N GLN* 2.9 32.1 + - - +
26N ALA* 1.3 77.9 - - - +
28N GLU* 1.3 62.7 + - - +
29N GLN* 4.2 1.7 + - - +
199N ALA 3.0 13.0 - - - -
203N LEU* 4.1 13.0 - - - -
205N HIS* 3.0 34.5 + - - +
208N LEU* 3.5 16.2 - - - -
379N ILE* 4.1 5.4 - - - -
12O GLU 4.4 2.1 + - - -
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Residues in contact with GLU 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N VAL* 4.4 13.1 - - - +
12N PRO* 3.8 36.3 - - + +
13N GLU 4.7 1.1 - - - +
14N THR* 4.2 6.5 - - - +
27N SER* 1.3 76.7 - - - +
29N GLN* 1.3 63.9 + - - +
30N SER* 3.8 4.7 + - - -
199N ALA 3.0 7.0 + - - -
200N ALA* 3.4 1.7 - - - +
201N GLY 3.0 25.5 + - - +
203N LEU* 5.7 0.7 - - - -
375N VAL* 3.6 23.9 - - + +
379N ILE* 3.8 15.9 - - + -
389N ARG* 2.9 26.0 + - - -
12O GLU 4.5 2.0 - - - +
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Residues in contact with GLN 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N PRO* 3.5 19.6 - - - +
27N SER* 4.2 1.4 + - - +
28N GLU* 1.3 73.9 - - - +
30N SER* 1.3 69.5 + - - +
201N GLY 3.3 4.7 - - - +
203N LEU 2.7 30.7 - - - +
204N GLU* 3.8 27.1 + - - +
205N HIS 4.8 2.2 + - - +
12O GLU* 2.7 38.9 + - - +
17O VAL* 3.8 27.6 + - - +
18O PRO* 3.4 20.6 - - + +
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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