Contacts of the strand formed by residues 306 - 309 (chain A) in PDB entry 1PS9
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 MET 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.8 21.3 - - + -
16A LEU* 3.7 31.9 - - + -
18A ASN 4.0 4.5 - - - +
19A ARG* 3.4 29.4 - - - +
20A VAL 3.9 16.8 - - - +
21A LEU* 3.9 14.6 - - + -
52A ALA* 5.1 0.2 - - + -
53A LEU* 5.2 1.8 - - + -
244A ILE* 4.7 9.4 - - - -
282A PRO* 5.5 0.9 - - + -
283A LEU 3.1 3.8 + - - +
284A VAL* 3.3 29.5 - - + -
285A THR 3.0 22.0 + - - -
299A LEU* 3.8 3.1 - - - -
304A ALA* 3.5 7.8 - - - +
305A ASP* 1.3 86.6 - - + +
307A VAL* 1.3 66.3 + - - +
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Residues in contact with VAL 307 (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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5A LEU* 4.1 12.3 - - + -
19A ARG 3.0 14.5 + - - +
20A VAL* 3.7 6.4 - - + +
21A LEU* 3.0 25.1 + - - +
284A VAL* 3.9 3.1 - - - -
285A THR* 3.5 7.6 - - + -
289A ILE* 4.1 14.6 - - + -
295A ALA* 3.9 26.7 - - + +
298A ILE* 4.0 19.7 - - + -
299A LEU* 4.0 21.1 - - + -
306A MET* 1.3 79.2 - - - +
308A SER* 1.3 58.7 + - - +
309A MET* 4.1 10.0 + - + -
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Residues in contact with SER 308 (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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21A LEU* 3.4 29.2 - - - +
23A GLY* 3.5 12.1 - - - -
214A ARG* 5.1 2.3 + - - -
246A ASN* 4.3 6.4 + - - -
284A VAL* 3.7 8.5 - - - +
285A THR 2.8 20.2 + - - +
286A THR* 3.7 24.7 + - - -
287A ASN 4.5 0.2 + - - -
289A ILE* 4.1 8.5 - - - +
307A VAL* 1.3 74.1 - - - +
309A MET* 1.3 70.6 + - - +
310A ALA* 4.8 0.7 + - - +
702A FMN 4.1 7.0 + - - -
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Residues in contact with MET 309 (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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5A LEU* 5.0 2.2 - - + -
20A VAL* 4.0 31.9 - - + -
21A LEU 3.1 6.0 + - - +
22A MET* 3.4 0.7 - - - -
23A GLY 3.1 12.9 + - - -
289A ILE* 3.0 41.3 - - + +
290A ASN* 4.4 6.5 - - - -
291A ASP 4.8 3.6 - - - +
292A PRO* 6.0 1.3 - - + -
295A ALA* 4.5 9.0 - - + -
307A VAL* 4.3 9.9 - - + -
308A SER* 1.3 80.2 + - - +
310A ALA* 1.3 60.3 + - - +
312A PRO* 4.2 7.6 - - + -
313A PHE* 3.0 29.8 - - + -
319A LEU* 4.0 26.2 - - + -
320A LEU* 4.9 6.3 - - + -
702A FMN 3.6 5.6 - - - -
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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