Contacts of the strand formed by residues 300 - 308 (chain B) in PDB entry 3HN8
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 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B GLY 5.1 2.6 + - - -
296B ALA 5.1 2.0 + - - -
298B CYS 3.5 17.4 + - - -
299B GLY* 1.3 75.5 - - - +
301B ILE* 1.3 62.2 + - - +
321B ALA* 3.3 2.9 - - - +
322B LEU* 2.8 55.2 + - + +
323B ASP* 3.4 29.5 + - - +
417B TRP* 3.9 25.2 - - + -
418B ARG 3.4 10.5 - - - +
419B ASP* 3.4 23.1 - - - +
420B ILE* 3.8 8.1 - - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ARG* 1.3 75.2 - - - +
302B SER* 1.3 68.5 + - - +
303B PHE* 4.2 20.8 - - + -
318B ILE* 4.0 25.8 - - + -
320B GLN 3.6 13.5 - - - +
321B ALA* 3.9 8.3 - - + -
337B VAL* 4.8 6.3 - - + -
362B PHE* 4.5 10.5 - - + -
382B PHE* 5.1 5.6 - - + -
384B VAL* 4.8 14.4 - - + -
399B VAL* 4.1 15.9 - - + -
416B LEU 4.2 0.3 - - - +
417B TRP* 3.5 4.4 - - - -
418B ARG 3.0 35.8 + - - +
420B ILE* 4.0 17.7 - - + -
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 1.3 76.5 - - - +
303B PHE* 1.3 67.7 + - - +
318B ILE* 4.0 0.3 - - - -
319B LEU* 2.9 35.6 + - - +
320B GLN* 2.8 22.5 + - - +
415B PRO* 4.8 5.5 - - - +
416B LEU 3.4 7.0 - - - -
417B TRP* 3.2 45.1 - - - -
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 4.2 23.3 - - + -
302B SER* 1.3 80.7 + - - +
304B ALA* 1.3 63.5 + - - +
305B LEU* 4.7 3.8 - - + -
316B VAL* 5.2 4.3 - - + -
317B ARG 2.8 24.7 - - - +
318B ILE* 3.8 5.2 - - + -
319B LEU* 3.5 11.1 - - - +
382B PHE* 3.2 35.9 - + - -
399B VAL* 4.6 2.7 - - + -
401B LEU* 3.5 35.2 - - + -
415B PRO* 3.7 2.8 - - - +
416B LEU* 3.1 62.7 + - + +
418B ARG* 4.1 13.5 - - + -
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B PHE* 1.3 78.9 - - - +
305B LEU* 1.3 65.7 + - - +
306B ARG* 4.5 14.7 + - - +
316B VAL* 3.7 1.2 - - - +
317B ARG* 2.8 35.4 + - + +
319B LEU* 4.3 10.0 - - + +
412B PRO* 6.4 0.2 - - + -
413B ASP* 5.3 14.8 - - - +
414B ARG 5.8 0.4 - - - +
415B PRO* 4.9 6.1 - - + -
416B LEU* 4.2 9.4 - - + -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B PHE* 4.7 6.1 - - + -
304B ALA* 1.3 79.9 - - - +
306B ARG* 1.3 64.6 + - - +
314B LEU* 4.0 17.5 - - + -
315B VAL 3.0 19.1 - - - +
316B VAL* 4.0 7.0 - - + -
380B LEU* 4.1 21.8 - - + -
401B LEU* 4.4 9.0 - - + -
404B LEU* 4.5 12.1 - - + +
407B LEU* 4.0 27.9 - - + +
408B ALA* 3.1 32.6 - - + +
411B PRO 5.1 4.5 - - - +
416B LEU* 4.2 23.2 - - + +
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ALA* 4.5 14.9 + - - +
305B LEU* 1.3 77.2 - - - +
307B TYR* 1.3 62.1 + - - +
308B LEU* 4.0 15.3 + - + +
313B GLN 4.0 0.3 - - - +
314B LEU* 4.0 1.8 - - - +
315B VAL* 2.9 50.8 + - + +
317B ARG* 3.9 36.8 - - - +
365B THR* 5.0 2.6 - - - +
408B ALA* 3.8 13.2 - - - +
412B PRO* 6.4 4.7 - - + -
413B ASP* 5.6 3.8 + - - -
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Residues in contact with TYR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B ARG* 1.3 75.2 - - - +
308B LEU* 1.3 58.7 + - - +
309B TYR* 3.0 53.4 + + + +
312B ASP* 3.5 14.1 + - - -
313B GLN 3.2 37.5 - - - -
314B LEU* 3.4 11.7 - - + -
370B VAL 2.7 25.5 + - - -
372B LEU* 3.0 45.1 + - + +
375B LEU* 3.9 22.9 - - + -
405B LEU* 5.0 3.1 - - + -
408B ALA* 3.8 17.2 + - + +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B ARG* 4.8 15.3 - - + +
307B TYR* 1.3 70.5 - - - +
309B TYR* 1.3 66.7 + - - +
311B SER* 3.5 12.1 + - - +
312B ASP* 3.4 2.9 + - - -
313B GLN* 3.0 49.2 + - + +
315B VAL* 3.8 25.6 - - + -
367B GLN* 5.2 2.7 - - - +
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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