Contacts of the strand formed by residues 347 - 354 (chain C) in PDB entry 5HP1
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 347 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315C HIS* 6.1 4.7 - - + -
317C VAL* 3.4 34.5 - - + +
342C TYR* 3.5 11.7 - - - +
343C GLN 4.4 2.4 + - - -
344C GLU* 3.6 15.8 + - - +
345C PRO 2.9 11.8 + - - +
346C PHE* 1.3 78.2 - - + +
348C ASN* 1.3 65.1 + - - +
349C LEU 3.3 2.9 + - - -
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Residues in contact with ASN 348 (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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270C ILE* 4.8 4.2 - - + +
272C PRO* 4.7 7.9 - - - +
315C HIS 4.2 4.1 + - - +
316C GLY* 3.3 9.2 - - - -
317C VAL* 3.2 17.5 + - - +
340C GLN* 3.5 29.4 - - - +
341C ILE 3.6 7.0 - - - +
342C TYR* 3.5 25.2 - - - -
346C PHE* 3.5 12.4 + - - +
347C LYS* 1.3 70.3 - - - +
349C LEU* 1.3 62.7 + - - +
350C LYS* 4.1 9.2 - - - +
351C THR* 4.0 12.1 - - + +
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Residues in contact with LEU 349 (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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98C ALA* 3.9 17.9 - - + +
239C TRP* 3.0 31.5 + - - -
316C GLY* 3.9 1.2 - - - -
317C VAL* 3.3 19.1 - - + +
318C TYR* 3.1 38.6 - - - +
319C TYR* 3.8 4.0 - - + +
325C LEU* 3.5 32.1 - - + -
341C ILE 2.9 11.2 + - - +
342C TYR* 4.3 8.5 - - - +
343C GLN* 3.6 21.3 - - + +
347C LYS 3.3 2.8 + - - -
348C ASN* 1.3 74.2 - - - +
350C LYS* 1.3 58.8 + - - +
383C TRP* 4.0 14.4 - - + +
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Residues in contact with LYS 350 (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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96C HIS* 3.5 40.6 - - + +
98C ALA* 4.8 0.4 - - + -
239C TRP* 4.4 1.1 - - + -
269C GLN* 3.5 17.9 + - - +
270C ILE* 4.5 6.5 - - - -
339C TYR* 4.4 1.4 + - - -
340C GLN* 3.7 0.5 - - - -
341C ILE* 2.9 40.4 + - + +
348C ASN* 3.4 3.4 - - - +
349C LEU* 1.3 82.1 - - - +
351C THR* 1.3 91.4 + - - +
352C GLY* 4.9 0.2 - - - -
378C GLU* 3.5 30.9 + - - +
382C ILE* 4.2 11.9 - - + -
383C TRP* 4.2 21.1 - - + -
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Residues in contact with THR 351 (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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268C SER 2.7 23.1 + - - -
269C GLN* 2.9 15.3 + - - +
270C ILE* 3.1 30.3 + - + +
271C TYR 3.8 0.2 + - - -
272C PRO* 3.9 26.9 - - + -
339C TYR* 3.3 19.3 - - - +
340C GLN* 4.0 5.4 - - + +
348C ASN* 4.0 18.6 - - + +
350C LYS* 1.3 102.7 + - - +
352C GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 352 (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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268C SER* 3.6 15.3 - - - -
269C GLN* 4.8 0.4 - - - -
338C THR* 3.3 8.6 - - - +
339C TYR* 3.0 48.5 + - - +
350C LYS* 4.9 0.7 - - - -
351C THR* 1.3 79.7 - - - +
353C LYS* 1.3 60.8 + - - -
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Residues in contact with LYS 353 (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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265C ASN* 3.0 22.4 - - - +
268C SER* 4.1 22.6 + - - +
274C ILE* 3.6 21.8 - - + +
275C LYS* 5.2 0.7 - - - -
276C VAL* 3.4 21.3 - - + +
332C GLN* 5.3 0.2 - - - +
337C TRP 3.2 12.3 - - - +
338C THR* 3.8 11.7 - - + -
339C TYR* 3.5 6.5 + - - -
352C GLY* 1.3 74.5 - - - +
354C TYR* 1.3 61.2 + - - +
355C ALA* 4.2 9.9 - - + +
374C LYS* 3.9 16.6 + - - -
6E C 3.1 20.5 + - - +
7E C 2.5 32.5 + - - -
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Residues in contact with TYR 354 (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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337C TRP* 2.8 51.4 + + + +
339C TYR* 4.4 6.1 - - + -
353C LYS* 1.3 73.5 - - - +
355C ALA* 1.3 61.8 + - - +
356C ARG* 3.5 51.3 + - + +
358C ARG* 4.6 5.9 + - - +
367C GLN* 3.8 21.3 - - + -
370C GLU* 3.0 37.4 + - + +
371C ALA* 3.6 28.0 - - + -
374C LYS* 3.7 31.6 - - + -
6E C 5.7 0.9 - - - -
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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