Contacts of the strand formed by residues 300 - 308 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295C GLY 5.1 3.2 + - - -
296C ALA 5.1 2.0 + - - -
298C CYS 3.5 17.6 + - - -
299C GLY* 1.3 73.2 - - - -
301C ILE* 1.3 59.2 + - - +
321C ALA* 3.3 3.1 - - - +
322C LEU* 2.8 61.0 + - + +
323C ASP* 3.4 30.1 + - - +
417C TRP* 3.9 24.9 - - + -
418C ARG 3.4 11.2 - - - +
419C ASP* 3.4 26.7 - - - +
420C ILE* 3.8 7.7 - - - +
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Residues in contact with ILE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C ARG* 1.3 76.2 - - - +
302C SER* 1.3 66.8 + - - +
303C PHE* 4.2 20.0 - - + -
318C ILE* 3.9 25.8 - - + -
320C GLN 3.6 13.5 - - - +
321C ALA* 3.9 9.0 - - + -
337C VAL* 4.9 5.6 - - + -
362C PHE* 4.5 11.4 - - + -
382C PHE* 5.1 6.1 - - + -
384C VAL* 4.8 15.3 - - + -
399C VAL* 4.2 14.8 - - + -
416C LEU 4.2 0.2 - - - +
417C TRP* 3.5 4.2 - - - -
418C ARG 3.0 36.1 + - - +
420C ILE* 4.0 18.4 - - + -
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Residues in contact with SER 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ILE* 1.3 76.4 - - - +
303C PHE* 1.3 67.7 + - - +
318C ILE* 4.0 0.3 - - - -
319C LEU* 2.9 35.6 + - - +
320C GLN* 2.8 23.3 + - - +
415C PRO* 4.8 5.3 - - - +
416C LEU 3.4 6.3 - - - -
417C TRP* 3.2 45.7 - - - -
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ILE* 4.2 23.6 - - + -
302C SER* 1.3 80.4 - - - +
304C ALA* 1.3 62.6 + - - +
305C LEU* 4.7 3.6 - - + -
316C VAL* 5.2 4.3 - - + -
317C ARG 2.8 25.8 - - - +
318C ILE* 3.9 4.9 - - + -
319C LEU* 3.5 12.3 - - - +
382C PHE* 3.2 35.0 - + - -
399C VAL* 4.6 3.1 - - + -
401C LEU* 3.6 34.5 - - + -
415C PRO* 3.7 2.4 - - - +
416C LEU* 3.1 62.3 + - + +
418C ARG* 4.1 13.5 - - + -
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Residues in contact with ALA 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C PHE* 1.3 78.6 - - - +
305C LEU* 1.3 65.9 + - - +
306C ARG* 4.5 15.3 + - - +
316C VAL* 3.7 1.2 - - - +
317C ARG* 2.8 34.8 + - + +
319C LEU* 4.3 10.0 - - + +
412C PRO* 6.5 1.1 - - + -
414C ARG 5.8 0.9 - - - +
415C PRO* 4.9 8.1 - - + -
416C LEU* 4.2 9.0 - - + -
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C PHE* 4.7 5.8 - - + -
304C ALA* 1.3 79.7 - - - +
306C ARG* 1.3 65.5 + - - +
314C LEU* 4.0 18.4 - - + -
315C VAL 3.0 19.3 - - - +
316C VAL* 4.0 6.7 - - + -
380C LEU* 4.1 22.0 - - + -
401C LEU* 4.4 8.3 - - + -
404C LEU* 4.5 11.9 - - + +
407C LEU* 4.0 28.7 - - + +
408C ALA* 3.1 33.1 - - + +
411C PRO 5.1 4.3 - - - +
416C LEU* 4.1 23.2 - - + +
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Residues in contact with ARG 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C ALA* 4.5 15.3 + - - +
305C LEU* 1.3 76.7 - - - +
307C TYR* 1.3 60.2 + - - +
308C LEU* 4.0 14.5 + - + +
313C GLN 4.0 0.3 - - - +
314C LEU* 4.0 1.4 - - - +
315C VAL* 2.9 49.7 + - + +
317C ARG* 3.9 36.8 - - - +
365C THR* 5.0 2.4 - - - +
408C ALA* 3.8 13.9 - - - +
412C PRO* 6.3 4.7 - - + -
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Residues in contact with TYR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C ARG* 1.3 75.5 - - - +
308C LEU* 1.3 58.7 + - - +
309C TYR* 3.1 55.8 + + + +
312C ASP* 3.5 13.4 + - - -
313C GLN 3.2 37.2 - - - -
314C LEU* 3.5 12.1 - - + -
370C VAL 2.7 26.2 + - - -
372C LEU* 3.1 45.2 + - + +
375C LEU* 3.9 23.3 - - + -
405C LEU* 5.0 3.1 - - + -
408C ALA* 3.9 16.8 + - + +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C ARG* 4.8 15.9 - - + +
307C TYR* 1.3 71.9 - - - +
309C TYR* 1.3 66.6 + - - +
311C SER* 3.5 12.5 + - - +
312C ASP* 3.4 3.3 + - - -
313C GLN* 3.0 47.8 + - + +
315C VAL* 3.8 25.6 - - + -
367C 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