Contacts of the strand formed by residues 361 - 368 (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 ILE 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319C LEU 3.7 5.8 - - - +
320C GLN* 3.5 30.3 - - + +
354C HIS* 3.0 21.9 + - + -
359C ASN 4.1 5.6 - - - +
360C PRO* 1.3 73.3 - - - +
362C PHE* 1.3 62.0 + - - +
363C ASN* 3.9 28.5 - - - +
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Residues in contact with PHE 362 (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* 4.5 4.7 - - + -
318C ILE* 3.6 33.7 - - + +
319C LEU 2.7 11.5 + - - +
320C GLN* 4.4 5.6 - - - -
321C ALA* 4.5 11.4 - - + -
324C LEU* 5.6 0.2 - - + -
335C PRO* 4.0 23.6 - - + -
336C TYR* 4.0 3.6 - - - -
337C VAL* 3.7 16.6 - - + -
351C THR* 3.5 34.8 - - + -
352C LYS* 6.1 0.3 - - - +
354C HIS* 3.8 25.2 - + - -
360C PRO* 3.6 32.3 - - + -
361C ILE* 1.3 71.6 - - - +
363C ASN* 1.3 70.5 + - - +
364C GLU* 3.1 16.9 + - - +
384C VAL* 5.6 4.7 - - + -
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Residues in contact with ASN 363 (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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317C ARG* 3.1 38.8 + - - +
318C ILE 2.9 12.1 + - - -
319C LEU* 3.2 18.3 + - - +
361C ILE* 3.9 22.2 - - - +
362C PHE* 1.3 75.3 - - - +
364C GLU* 1.3 58.3 + - - +
365C THR 4.3 0.2 + - - -
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Residues in contact with GLU 364 (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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317C ARG* 3.3 2.8 - - - -
318C ILE* 2.9 29.6 + - + +
350C GLN 3.8 2.9 - - - +
351C THR* 3.2 29.5 - - + -
352C LYS* 2.7 47.6 + - + +
354C HIS* 4.4 3.8 - - - -
362C PHE* 3.1 16.8 - - + +
363C ASN* 1.3 79.2 - - - +
365C THR* 1.3 63.9 + - - +
366C PHE* 3.8 23.2 - - + -
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Residues in contact with THR 365 (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* 5.0 3.1 - - - +
315C VAL* 3.5 27.4 - - + -
316C VAL 3.3 4.9 - - - +
317C ARG* 2.9 45.3 + - + +
364C GLU* 1.3 72.6 - - - +
366C PHE* 1.3 78.0 + - - +
367C GLN* 5.5 6.7 - - - +
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Residues in contact with PHE 366 (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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314C LEU 3.7 1.6 - - - +
315C VAL* 3.3 3.6 - - - -
316C VAL* 2.8 47.2 + - + +
318C ILE* 4.4 4.9 - - + -
339C ILE* 3.7 23.1 - - + -
349C PHE* 3.3 54.1 - + + -
350C GLN 4.0 11.4 - - - -
351C THR* 3.9 17.3 - - + -
364C GLU* 3.8 43.7 - - + -
365C THR* 1.3 81.0 - - - +
367C GLN* 1.3 65.2 + - - +
368C PHE* 4.2 9.4 - - + -
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Residues in contact with GLN 367 (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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308C LEU* 5.2 1.9 - - - +
313C GLN* 3.0 37.6 + - - +
314C LEU 3.6 3.8 - - - -
315C VAL* 4.3 20.4 - - + +
347C LYS* 5.4 0.9 + - - -
349C PHE* 3.7 22.7 - - - -
365C THR* 5.5 4.9 - - + +
366C PHE* 1.3 79.4 - - - +
368C PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 368 (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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313C GLN* 3.1 10.3 - - - -
314C LEU* 2.8 52.6 + - + +
316C VAL* 4.4 14.8 - - + -
339C ILE* 3.8 21.3 - - + -
341C LEU* 3.9 23.8 - - + -
347C LYS* 3.3 40.2 - - + +
349C PHE* 3.6 32.5 - + - -
366C PHE* 4.2 15.0 - - + -
367C GLN* 1.3 78.3 - - - +
369C SER* 1.3 60.1 + - - +
370C VAL* 3.5 11.0 + - + -
380C LEU* 4.2 15.3 - - + -
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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