Contacts of the strand formed by residues 23 - 28 (chain H) in PDB entry 6PSS
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 HIS 23 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H GLN* 3.7 4.0 - - - +
19H VAL* 3.4 39.1 + - + +
20H SER* 2.9 36.8 - - - +
21H SER 3.4 2.6 + - - -
22H THR* 1.3 80.4 - - + +
24H ALA* 1.3 75.4 + - - +
25H LYS* 5.4 3.7 - - + -
204H GLU* 3.6 37.7 + - + -
205H MET 3.1 10.6 + - - -
206H GLU* 3.4 23.5 + - + +
213H PRO* 3.8 5.1 - - - +
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Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 4.1 15.3 - - + -
17H GLU 3.3 14.1 - - - +
18H GLN* 4.1 7.0 - - - +
19H VAL* 4.9 1.3 - - - +
23H HIS* 1.3 83.5 + - - +
25H LYS* 1.3 62.5 + - - +
26H VAL* 4.0 8.7 - - + -
204H GLU* 3.5 1.7 - - - -
205H MET* 2.9 34.7 + - + +
213H PRO* 3.7 23.9 - - + +
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Residues in contact with LYS 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ASP 3.7 3.8 - - - +
17H GLU* 3.1 51.5 + - + +
19H VAL* 5.4 9.2 - - + -
23H HIS* 5.4 3.8 - - + -
24H ALA* 1.3 77.5 - - - +
26H VAL* 1.3 61.0 + - - +
27H THR* 3.7 5.0 + - - +
202H VAL* 4.7 18.8 - - + +
203H ILE 3.4 9.4 - - - +
204H GLU* 3.8 30.6 + - + +
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Residues in contact with VAL 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G PHE* 5.0 0.9 - - + -
234G LEU* 4.7 6.7 - - + -
14H VAL* 3.9 25.1 - - + -
15H ASP 4.1 3.8 - - - -
16H ILE* 3.8 31.6 - - + +
24H ALA* 4.4 10.3 - - + -
25H LYS* 1.3 70.2 - - - +
27H THR* 1.3 66.7 + - - +
28H LEU* 4.3 11.8 - - + +
201H LEU 3.9 0.5 - - - +
202H VAL 3.1 3.1 - - - -
203H ILE* 2.6 43.2 + - + +
205H MET* 5.7 1.3 - - + -
213H PRO 5.5 2.2 - - - +
214H GLU* 5.9 0.4 - - - -
217H ILE* 3.8 31.9 - - + -
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Residues in contact with THR 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H VAL* 3.2 26.7 - - - +
15H ASP* 3.5 31.7 + - - +
25H LYS* 3.7 9.7 + - - +
26H VAL* 1.3 76.9 + - - +
28H LEU* 1.3 71.8 + - - +
29H GLU* 4.2 2.2 - - + +
200H LYS* 3.7 30.7 - - - +
201H LEU 3.3 8.1 - - - +
202H VAL* 3.9 18.1 - - + +
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Residues in contact with LEU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ALA 5.8 0.7 - - - +
231G PHE* 3.6 51.1 - - + -
234G LEU* 5.5 1.1 - - + -
11H PRO* 3.7 33.0 - - + -
13H LEU 3.6 5.8 - - - -
14H VAL* 4.7 11.2 - - + -
26H VAL* 4.3 10.3 - - + +
27H THR* 1.3 81.9 - - - +
29H GLU* 1.3 67.2 + - - +
30H PRO* 3.7 5.5 - - - +
31H LEU* 4.3 11.7 - - + +
39H LEU* 5.9 0.2 - - + -
200H LYS* 3.5 2.5 - - - -
201H LEU* 2.8 49.1 + - + +
203H ILE* 4.9 1.8 - - + -
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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