Contacts of the strand formed by residues 345 - 349 (chain B) in PDB entry 3HN3
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 PHE 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336B PHE* 3.9 33.2 - + + -
343B PHE* 3.8 19.3 - + - -
344B TYR* 1.3 76.3 - - - +
346B HIS* 1.3 59.5 + - - +
347B GLY 3.9 0.2 - - - -
379B ASN* 3.7 4.7 - - - -
380B ALA* 3.6 20.6 - - + -
402B VAL* 3.7 18.6 - - + -
404B ILE* 4.0 26.2 - - + -
444B VAL* 3.8 22.4 - - + -
445B MET* 4.8 0.9 - - + -
537B ILE* 3.9 21.3 - - + -
582B VAL 2.9 20.2 + - - -
583B GLY* 3.2 10.8 - - - -
584B GLU 2.8 27.3 + - - +
585B LEU* 4.4 12.3 - - + -
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Residues in contact with HIS 346 (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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292B LEU* 4.5 5.9 - - + +
344B TYR* 3.4 29.4 - + + -
345B PHE* 1.3 73.2 - - - +
347B GLY* 1.3 57.1 + - - +
377B GLY 3.0 23.6 + - - -
378B ALA* 3.3 5.2 - - - -
379B ASN* 2.8 48.2 + - + -
584B GLU* 3.7 4.0 - - + -
626B TYR* 3.4 41.6 - + + +
629B ILE* 3.9 25.4 - - + -
630B ALA* 4.1 21.5 - - + +
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Residues in contact with GLY 347 (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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345B PHE 3.9 0.2 - - - -
346B HIS* 1.3 76.6 - - - +
348B VAL* 1.3 68.8 + - - +
378B ALA* 4.2 4.3 - - - -
380B ALA* 3.2 16.8 - - - -
584B GLU 3.1 8.9 + - - -
585B LEU* 3.8 12.1 - - - +
586B ILE* 3.3 10.0 + - - +
626B TYR* 2.6 26.6 + - - -
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Residues in contact with VAL 348 (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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347B GLY* 1.3 80.9 - - - +
349B ASN* 1.3 74.6 + - - +
350B LYS* 3.8 9.0 - - + -
373B LEU* 3.6 25.4 - - + -
376B LEU* 3.7 28.3 - - + -
378B ALA* 4.6 1.8 - - + -
380B ALA 3.1 3.0 + - - -
381B PHE* 3.0 36.6 - - + +
382B ARG 3.2 3.5 + - - -
585B LEU* 3.8 6.0 - - - +
586B ILE* 3.7 24.7 - - + +
589B PHE* 4.0 11.4 - - + -
608B ILE* 4.6 3.8 - - + -
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Residues in contact with ASN 349 (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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348B VAL* 1.3 75.4 - - - +
350B LYS* 1.3 60.9 + - - +
382B ARG* 2.9 41.9 + - - +
384B SER* 3.4 8.0 + - - +
539B SER 2.8 23.7 + - - +
540B GLU* 3.9 0.2 - - - +
585B LEU* 3.4 9.7 + - - +
586B ILE 3.0 26.8 + - - +
587B TRP* 3.3 33.0 - - + +
588B ASN* 3.3 3.0 - - - +
589B PHE* 2.9 29.6 + - - +
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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