Contacts of the strand formed by residues 295 - 302 (chain A) in PDB entry 3INB
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 LYS 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A MET* 3.3 11.3 - - - +
257A VAL* 5.1 0.4 - - - -
291A LEU* 3.4 0.9 - - - -
292A GLY 3.2 23.0 + - - +
293A GLU* 3.2 41.6 + - - +
294A LEU* 1.3 79.9 - - - +
296A LEU* 1.3 63.5 + - - +
323A LYS* 4.2 28.3 - - + +
324A LEU 3.5 15.0 - - - +
325A GLY* 4.0 6.7 - - - -
326A VAL 4.3 1.1 - - - +
358A ILE* 3.1 24.5 - - + +
361A ASN* 4.1 13.7 + - - -
417A LEU* 4.3 10.7 - - + +
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Residues in contact with LEU 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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229A GLY* 3.9 4.0 - - - -
230A GLY 3.5 21.1 - - - +
255A PHE* 4.8 8.1 - - + -
256A GLU 2.8 34.3 - - - +
257A VAL* 3.5 19.6 - - + +
289A VAL* 3.3 20.9 - - + -
290A ALA 3.4 5.4 - - - +
291A LEU* 3.5 4.9 - - + -
295A LYS* 1.3 73.8 - - - +
297A ALA* 1.3 97.5 + - - +
298A ALA* 4.2 6.3 - - + +
322A VAL* 4.3 3.2 - - + +
323A LYS* 3.5 3.8 + - - +
324A LEU* 3.0 41.7 + - + +
358A ILE* 4.1 0.4 - - - -
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Residues in contact with ALA 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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288A MET 3.7 0.2 - - - +
289A VAL* 3.6 0.2 - - - -
290A ALA* 2.8 25.6 + - + +
296A LEU* 1.3 88.8 - - - +
298A ALA* 1.3 62.2 + - - +
321A LEU* 4.8 1.6 - - + -
322A VAL* 3.7 8.5 - - - +
323A LYS* 4.6 0.9 - - - +
358A ILE* 3.6 24.5 - - + +
363A ALA* 4.2 5.6 - - + -
365A TRP* 3.7 15.2 - - + -
417A LEU* 4.3 16.4 - - + -
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Residues in contact with ALA 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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231A THR* 5.5 2.2 - - + -
255A PHE* 4.2 27.6 - - + -
287A CYS* 5.1 2.0 - - + -
288A MET 2.9 14.8 - - - +
289A VAL* 4.7 4.0 - - + -
296A LEU* 4.4 8.1 - - + -
297A ALA* 1.3 77.8 - - - +
299A LEU* 1.3 62.1 + - - +
300A CYS* 4.1 5.6 - - - -
320A GLN 4.2 0.2 - - - -
321A LEU* 3.3 10.2 - - - +
322A VAL* 3.1 32.2 + - + -
365A TRP* 4.2 4.0 - - - -
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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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286A ASN 3.8 1.0 - - - +
287A CYS* 3.5 0.7 - - - -
288A MET* 2.9 52.9 + - + +
298A ALA* 1.3 74.1 - - - +
300A CYS* 1.3 63.1 + - - +
319A PHE* 3.5 25.2 - - + -
320A GLN 3.3 14.1 - - - +
321A LEU* 3.6 25.1 - - + -
351A LEU* 6.2 0.2 - - - +
365A TRP* 3.8 26.7 - - + -
413A LEU* 4.6 2.2 - - + -
415A VAL* 3.9 7.2 - - + -
425A ILE* 3.5 43.5 - - + -
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Residues in contact with CYS 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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253A ARG* 4.9 0.2 - - - -
255A PHE* 3.4 25.1 - - - -
278A GLN* 6.0 0.2 - - - -
285A SER* 5.6 2.7 - - - -
286A ASN 3.5 4.9 - - - +
287A CYS* 2.0 44.6 - - - -
298A ALA* 4.6 1.3 - - - -
299A LEU* 1.3 79.3 - - - +
301A HIS* 1.3 64.6 + - - +
319A PHE* 3.4 10.0 - - - +
320A GLN* 2.8 48.4 + - + +
322A VAL* 5.2 0.9 - - - -
336A TRP* 5.4 0.7 - - - -
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Residues in contact with HIS 301 (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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285A SER* 3.2 5.1 - - - -
286A ASN 2.7 39.4 + - - +
300A CYS* 1.3 79.4 - - - +
302A GLY* 1.3 89.5 + - - +
303A GLU* 3.5 25.9 + - + +
304A ASP* 4.6 1.8 - - - -
306A ILE* 3.1 45.7 - - + +
317A VAL* 4.6 8.7 - - + -
318A SER 3.6 19.8 + - - -
319A PHE* 4.0 12.9 - - + -
336A TRP* 6.1 3.0 - - - -
351A LEU* 4.5 5.6 - - + -
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Residues in contact with GLY 302 (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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284A LEU* 3.8 7.0 - - - -
285A SER* 4.3 4.7 - - - -
301A HIS* 1.3 87.7 + - - +
303A GLU* 1.3 77.1 - - - +
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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