Contacts of the strand formed by residues 289 - 296 (chain A) in PDB entry 3RN5
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 GLY 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ILE* 3.1 22.9 - - - +
256A GLN* 5.2 3.1 - - - -
285A SER* 3.3 3.6 - - - -
286A ASP* 3.1 20.5 + - - +
287A ASN 3.5 0.2 - - - -
288A THR* 1.3 83.7 + - - +
290A LYS* 1.3 64.9 + - - -
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Residues in contact with LYS 290 (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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252A ILE* 3.6 11.0 - - - +
256A GLN* 4.3 6.3 + - - +
271A GLN* 3.5 31.4 + - - +
283A ASP* 4.9 14.7 + - - +
284A LEU 3.4 7.6 - - - +
285A SER* 4.8 3.8 - - - -
289A GLY* 1.3 77.3 - - - +
291A MET* 1.3 65.1 + - - +
323A LYS* 4.3 9.8 + - + -
324A LEU* 3.6 6.6 - - - +
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Residues in contact with MET 291 (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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252A ILE* 3.8 16.4 - - + -
255A LEU* 3.7 10.1 - - + -
268A PHE* 3.9 32.8 - - + -
282A PHE 3.7 0.3 - - - +
283A ASP* 3.5 2.2 - - - -
284A LEU* 2.8 41.6 + - + +
290A LYS* 1.3 77.3 - - - +
292A GLU* 1.3 62.8 + - - +
293A VAL* 4.2 13.0 - - + -
312A LEU* 5.1 0.2 - - + -
323A LYS* 5.2 1.3 - - - +
324A LEU* 3.2 51.4 - - + +
326A LEU* 3.4 34.1 - - + -
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Residues in contact with GLU 292 (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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281A LEU* 3.6 31.3 - - + +
282A PHE 3.2 4.3 - - - -
283A ASP* 2.6 25.6 - - - +
291A MET* 1.3 75.2 - - - +
293A VAL* 1.3 64.9 + - - +
319A LYS* 5.7 2.8 + - - -
323A LYS* 4.9 20.5 - - + +
324A LEU 3.2 7.0 + - - +
325A GLN* 2.9 25.1 + - + +
326A LEU 2.9 23.4 + - - -
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Residues in contact with VAL 293 (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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280A ILE 3.3 2.6 - - - +
281A LEU* 3.5 3.7 - - - +
282A PHE* 2.6 54.4 + - + +
284A LEU* 4.1 20.9 - - + -
291A MET* 4.2 13.9 - - + -
292A GLU* 1.3 82.8 - - - +
294A LEU* 1.3 58.9 + - - +
295A GLY* 3.7 1.4 + - - +
312A LEU* 4.3 9.9 - - + -
315A PHE* 3.3 34.8 - - + -
325A GLN* 4.3 0.2 - - - -
326A LEU* 3.0 32.1 - - + +
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Residues in contact with LEU 294 (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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276A LYS* 3.9 19.5 - - + -
279A ASN* 4.0 18.2 + - + +
280A ILE 3.4 6.3 - - - +
281A LEU* 3.6 37.5 - - + +
293A VAL* 1.3 69.9 - - - +
295A GLY* 1.3 60.8 + - - +
315A PHE* 3.7 2.8 - - - -
325A GLN* 3.3 26.7 - - - +
326A LEU 3.1 8.0 + - - +
327A THR* 4.8 6.7 - - + -
328A SER* 3.0 28.9 + - - -
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Residues in contact with GLY 295 (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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279A ASN* 2.7 37.2 + - - +
280A ILE* 3.1 14.5 + - - -
282A PHE* 5.1 7.9 - - - -
293A VAL* 3.7 3.0 + - - +
294A LEU* 1.3 72.8 - - - +
296A VAL* 1.3 58.2 + - - -
315A PHE* 4.1 12.3 - - - -
328A SER* 3.7 12.1 - - - -
334A ILE* 6.0 3.6 - - - -
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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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278A LYS 4.8 0.7 - - - -
279A ASN* 4.0 8.5 - - - +
280A ILE* 4.4 5.2 - - - +
282A PHE* 5.5 0.9 - - - -
295A GLY* 1.3 74.8 - - - -
297A ARG* 1.3 60.5 + - - +
298A ASN* 3.5 22.9 - - - +
301A THR* 3.0 27.9 + - + +
315A PHE* 5.5 0.2 - - - -
328A SER* 4.1 15.9 + - - +
329A GLY 6.0 0.2 - - - +
334A ILE* 4.5 12.9 - - + +
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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