Contacts of the strand formed by residues 300 - 308 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A GLY 5.1 3.2 + - - -
296A ALA 5.1 2.2 + - - -
298A CYS 3.5 17.4 + - - -
299A GLY* 1.3 73.7 - - - -
301A ILE* 1.3 59.4 + - - +
321A ALA* 3.3 2.8 - - - +
322A LEU* 2.8 57.9 + - + +
323A ASP* 3.4 29.5 + - - +
417A TRP* 3.9 24.8 - - + -
418A ARG 3.4 11.2 - - - +
419A ASP* 3.4 24.9 - - - +
420A ILE* 3.8 8.3 - - - +
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Residues in contact with ILE 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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300A ARG* 1.3 75.8 - - - +
302A SER* 1.3 68.4 + - - +
303A PHE* 4.2 19.9 - - + -
318A ILE* 3.9 26.7 - - + -
320A GLN 3.6 13.7 - - - +
321A ALA* 3.9 8.7 - - + -
337A VAL* 4.8 5.6 - - + -
362A PHE* 4.4 10.8 - - + -
382A PHE* 5.1 5.6 - - + -
384A VAL* 4.8 16.2 - - + -
399A VAL* 4.1 15.0 - - + -
416A LEU 4.2 0.3 - - - +
417A TRP* 3.5 4.6 - - - -
418A ARG 3.0 35.9 + - - +
420A ILE* 4.0 18.6 - - + -
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Residues in contact with SER 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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301A ILE* 1.3 75.6 - - - +
303A PHE* 1.3 68.3 + - - +
318A ILE* 4.2 0.2 - - - -
319A LEU* 2.9 35.7 + - - +
320A GLN* 2.8 22.5 + - - +
415A PRO* 4.8 4.8 - - - +
416A LEU 3.4 6.7 - - - -
417A TRP* 3.2 46.8 - - - -
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Residues in contact with PHE 303 (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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301A ILE* 4.2 22.9 - - + -
302A SER* 1.3 81.5 - - - +
304A ALA* 1.3 64.4 + - - +
305A LEU* 4.7 3.8 - - + -
316A VAL* 5.2 3.6 - - + -
317A ARG 2.8 24.5 - - - +
318A ILE* 3.8 5.6 - - + -
319A LEU* 3.5 11.6 - - - +
382A PHE* 3.2 35.9 - + - -
399A VAL* 4.6 2.7 - - + -
401A LEU* 3.5 35.0 - - + -
415A PRO* 3.7 2.8 - - - +
416A LEU* 3.1 61.2 + - + +
418A ARG* 4.1 13.7 - - + -
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Residues in contact with ALA 304 (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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303A PHE* 1.3 78.9 - - - +
305A LEU* 1.3 65.9 + - - +
306A ARG* 4.5 14.4 + - - +
316A VAL* 3.7 1.2 - - - +
317A ARG* 2.8 35.2 + - + +
319A LEU* 4.3 10.5 - - + +
413A ASP* 4.8 20.0 - - - +
414A ARG 5.8 0.2 - - - +
415A PRO* 4.9 6.1 - - + -
416A LEU* 4.2 10.1 - - + -
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Residues in contact with LEU 305 (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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303A PHE* 4.7 6.1 - - + -
304A ALA* 1.3 80.7 - - - +
306A ARG* 1.3 64.1 + - - +
314A LEU* 4.0 18.4 - - + -
315A VAL 3.0 18.6 - - - +
316A VAL* 4.0 6.1 - - + -
317A ARG 4.8 0.2 - - - +
380A LEU* 4.1 21.8 - - + -
401A LEU* 4.4 9.2 - - + -
404A LEU* 4.5 11.4 - - + +
407A LEU* 4.0 28.7 - - + +
408A ALA* 3.1 32.4 - - + +
411A PRO 5.1 4.2 - - - +
416A LEU* 4.2 22.5 - - + +
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Residues in contact with ARG 306 (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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304A ALA* 4.5 15.3 + - - +
305A LEU* 1.3 75.9 - - - +
307A TYR* 1.3 60.7 + - - +
308A LEU* 4.0 15.7 + - + +
313A GLN 4.0 0.5 - - - +
314A LEU* 4.0 1.2 - - - +
315A VAL* 2.9 50.1 + - + +
317A ARG* 3.9 38.8 - - - +
365A THR* 5.0 1.8 - - - +
408A ALA* 3.8 14.4 - - - +
412A PRO* 6.4 3.6 - - + -
413A ASP* 6.0 0.2 + - - -
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Residues in contact with TYR 307 (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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306A ARG* 1.3 74.9 - - - +
308A LEU* 1.3 57.9 + - - +
309A TYR* 3.0 53.8 + + + +
312A ASP* 3.5 14.5 + - - -
313A GLN 3.3 36.3 - - - -
314A LEU* 3.4 12.6 - - + -
370A VAL* 2.7 25.7 + - + -
372A LEU* 3.1 44.4 + - + +
375A LEU* 3.8 22.7 - - + -
405A LEU* 5.0 3.4 - - + -
408A ALA* 3.9 16.6 + - + +
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Residues in contact with LEU 308 (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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306A ARG* 4.8 16.8 - - + +
307A TYR* 1.3 70.4 - - - +
309A TYR* 1.3 66.8 + - - +
311A SER* 3.5 11.4 + - - +
312A ASP* 3.4 2.6 + - - -
313A GLN* 3.0 49.4 + - + +
315A VAL* 3.8 26.0 - - + -
367A GLN* 5.2 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