Contacts of the strand formed by residues 295 - 300 (chain A) in PDB entry 1PJS
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ARG* 3.3 27.8 - - - +
180A GLU* 2.7 31.4 + - - -
216A GLY* 5.1 0.4 - - - -
217A GLU* 3.1 37.1 + - + +
219A VAL* 5.5 1.1 - - + -
237A GLN* 5.7 0.2 - - - +
238A GLN* 4.3 19.8 + - - +
241A GLN* 3.4 43.7 + - - +
242A ALA* 3.8 7.4 - - + +
243A ASP* 2.7 43.3 + - - +
244A ILE* 3.4 6.9 + - - +
294A LYS* 1.3 71.2 - - - +
296A VAL* 1.3 62.9 + - - +
297A VAL* 5.8 2.0 - - + -
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Residues in contact with VAL 296 (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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217A GLU 2.8 19.6 + - - +
218A VAL* 3.5 7.8 - - + -
219A VAL* 3.0 27.5 + - - +
244A ILE* 3.5 15.5 - - + +
246A VAL* 4.1 14.8 - - + -
286A LEU* 3.4 38.4 - - + +
289A GLU* 3.5 31.9 - - + -
290A ALA* 3.8 11.7 - - - +
294A LYS 4.1 2.2 - - - +
295A ARG* 1.3 75.4 - - - +
297A VAL* 1.3 68.1 + - - +
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Residues in contact with VAL 297 (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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219A VAL* 3.4 15.9 - - + +
221A VAL* 3.9 19.5 - - + -
238A GLN* 3.5 35.0 - - + +
239A ILE* 4.2 15.7 - - + -
242A ALA* 3.5 11.9 - - + -
244A ILE 3.1 6.9 + - - -
245A VAL* 3.3 17.3 - - + +
246A VAL 2.8 26.2 + - - -
295A ARG* 4.8 3.1 - - + +
296A VAL* 1.3 80.4 - - - +
298A ARG* 1.3 60.5 + - - +
299A LEU* 3.4 10.7 + - - +
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Residues in contact with ARG 298 (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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218A VAL* 4.9 1.8 - - + +
219A VAL 3.0 8.2 + - - +
220A LEU* 3.2 26.5 - - + +
221A VAL 3.0 22.8 + - - +
246A VAL* 3.3 40.4 + - - -
247A TYR 4.0 0.8 - - - -
248A ASP* 3.8 24.0 + - - +
268A VAL* 4.3 17.4 - - - +
279A GLN* 4.6 2.6 + - - -
282A ILE* 3.7 12.8 - - - +
286A LEU* 4.1 15.7 - - + -
296A VAL* 4.2 1.4 - - - +
297A VAL* 1.3 69.8 - - - +
299A LEU* 1.3 77.5 + - - +
300A LYS* 3.4 21.2 + - - +
313A GLU* 3.0 39.2 + - - +
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Residues in contact with LEU 299 (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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221A VAL* 3.6 16.8 - - + +
223A ALA* 3.2 36.3 - - + -
231A LEU* 6.2 1.1 - - + -
239A ILE* 4.4 15.0 - - + -
245A VAL* 3.9 19.3 - - + -
246A VAL 2.8 14.4 + - - +
247A TYR* 3.5 6.3 - - + -
248A ASP 3.7 0.7 + - - -
251A VAL* 3.4 33.7 - - + +
255A ILE* 4.2 10.1 - - + -
256A MET* 3.6 18.8 - - - -
259A VAL* 4.3 9.2 - - + -
297A VAL* 3.4 5.6 + - + -
298A ARG* 1.3 83.3 + - - +
300A LYS* 1.3 60.5 + - - +
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Residues in contact with LYS 300 (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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220A LEU* 4.4 2.9 - - + -
221A VAL 3.1 9.9 + - - +
222A GLY* 3.8 1.4 - - - -
223A ALA* 2.9 29.5 + - - +
248A ASP* 3.5 8.5 - - - +
251A VAL* 4.3 1.6 - - - -
279A GLN* 4.6 0.4 + - - -
298A ARG* 3.4 36.5 + - + +
299A LEU* 1.3 72.6 - - - +
301A GLY* 1.3 66.6 + - - +
304A PRO* 4.5 25.8 - - + -
308A GLY* 4.7 5.2 - - - -
309A ARG* 3.0 16.0 - - - +
310A GLY* 2.9 33.9 - - - +
313A GLU* 2.5 38.5 + - - -
501A SAH 5.9 0.4 - - - +
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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