Contacts of the helix formed by residues 311 - 316 (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 ARG 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A MET* 4.1 6.7 - - - -
259A ILE* 2.8 46.8 + - - +
288A ARG* 4.0 11.9 - - - +
310A ALA* 1.3 78.1 - - - +
312A PRO* 1.3 67.4 - - + +
313A PHE 2.9 0.2 - - - -
314A LEU* 2.8 16.4 + - + +
315A ALA* 3.1 9.4 + - - +
334A CYS* 3.6 15.4 - - - -
336A GLY* 3.4 18.5 - - - -
338A ASN* 2.8 28.6 + - - -
341A CYS* 3.8 1.8 - - - -
700A SF4 3.6 29.3 - - - -
702A FMN 2.7 72.9 + - + +
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Residues in contact with PRO 312 (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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289A ILE 3.4 23.6 - - - +
290A ASN* 3.8 20.9 - - + +
309A MET* 4.2 5.4 - - + -
310A ALA 3.3 13.7 - - - +
311A ARG* 1.3 93.4 - - + +
313A PHE* 1.3 56.7 + - - +
315A ALA* 3.6 2.5 + - + +
316A ASP* 3.0 28.1 + - - +
319A LEU* 3.6 27.3 - - + +
332A ASN 4.9 0.7 - - - +
334A CYS* 3.8 16.8 - - + +
702A FMN 3.9 10.3 - - - +
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Residues in contact with PHE 313 (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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20A VAL* 3.8 28.0 - - + -
22A MET* 3.5 36.6 - - + -
46A ARG* 2.7 51.7 + - + -
49A HIS 5.9 0.2 - - - -
51A VAL* 3.5 22.9 - - + -
309A MET* 3.0 36.1 - - + -
310A ALA 2.9 10.6 + - - +
312A PRO* 1.3 77.6 - - - +
314A LEU* 1.3 55.9 + - - +
316A ASP 3.9 12.8 - - - -
317A ALA 3.8 11.0 + - - -
319A LEU* 4.0 24.5 - - + -
320A LEU* 4.1 13.2 - - + -
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Residues in contact with LEU 314 (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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25A MET* 3.4 45.5 - - + -
27A THR* 5.8 1.1 - - + -
42A PHE* 3.5 26.0 - - + -
46A ARG* 3.8 4.2 + - - +
311A ARG* 2.8 10.6 + - + +
313A PHE* 1.3 78.3 - - - +
315A ALA* 1.3 60.7 + - - +
316A ASP 3.5 0.2 + - - -
341A CYS* 3.9 28.3 - - + -
351A THR* 4.8 8.1 - - - +
352A SER 4.2 5.6 - - - +
353A CYS* 4.2 4.9 - - + -
356A ASN* 2.9 26.3 + - - +
359A ALA* 3.4 19.3 - - + +
360A CYS* 4.6 7.4 - - - -
700A SF4 4.1 11.4 - - - -
702A FMN 5.1 2.0 - - + -
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Residues in contact with ALA 315 (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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311A ARG 3.1 7.9 + - - +
312A PRO 3.7 7.2 - - - +
314A LEU* 1.3 82.0 - - - +
316A ASP* 1.3 61.0 + - - +
332A ASN* 3.3 39.5 + - - +
334A CYS* 3.8 23.6 - - + +
353A CYS* 3.6 15.8 - - - -
355A VAL* 3.9 9.9 - - + -
356A ASN* 3.5 9.5 + - - +
700A SF4 4.6 0.2 - - - -
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Residues in contact with ASP 316 (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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312A PRO 3.0 18.7 + - - +
313A PHE* 3.8 6.1 - - - -
314A LEU 3.3 0.6 - - - -
315A ALA* 1.3 79.3 - - - +
317A ALA* 1.3 64.5 + - - +
318A GLU* 2.9 31.2 + - - +
319A LEU* 3.2 24.7 + - + +
322A LYS* 2.8 28.4 + - - +
331A ILE* 3.5 7.5 - - + -
332A ASN* 3.0 31.8 + - - +
356A ASN* 4.9 2.0 - - - +
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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