Contacts of the strand formed by residues 413 - 417 (chain B) in PDB entry 1HNI
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 GLU 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B ARG* 4.3 23.3 + - + +
82B LYS* 3.3 38.8 + - + +
386B THR* 5.4 3.9 + - - +
387B PRO 3.7 5.1 + - - +
388B LYS* 3.3 26.2 - - + +
389B PHE* 2.7 31.6 + - - +
411B ILE 3.6 0.6 + - - -
412B PRO* 1.3 72.4 - - - +
414B TRP* 1.3 62.0 + - - +
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Residues in contact with TRP 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 3.0 39.1 - - - +
372B VAL* 4.9 2.9 - - + -
388B LYS* 5.7 2.0 - - - -
389B PHE* 3.5 10.8 - - + +
391B LEU* 3.9 20.6 - - + -
398B TRP* 3.3 46.9 - + - +
399B GLU* 3.5 20.2 + - - -
402B TRP* 3.6 28.3 - + - -
406B TRP* 5.0 4.0 - + - -
411B ILE* 3.5 17.0 - - + -
412B PRO* 3.5 22.0 - - + -
413B GLU* 1.3 84.4 + - - +
415B GLU* 1.3 65.1 + - - +
416B PHE* 3.9 15.8 - + - -
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LYS* 3.7 27.4 + - - -
389B PHE 2.9 18.7 + - - +
390B LYS* 2.7 38.8 + - + +
391B LEU* 3.2 22.9 + - - +
414B TRP* 1.3 76.6 - - - +
416B PHE* 1.3 76.2 + - - +
417B VAL* 5.2 1.4 - - - +
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Residues in contact with PHE 416 (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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391B LEU* 3.7 11.9 - - + -
393B ILE* 3.3 35.2 - - + +
395B LYS* 3.8 38.6 - - + +
398B TRP* 3.3 46.7 - + + -
399B GLU* 4.0 10.8 - - - -
414B TRP* 3.9 22.0 - + - -
415B GLU* 1.3 85.4 - - - +
417B VAL* 1.3 63.6 + - - +
418B ASN* 4.0 5.2 + - - +
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Residues in contact with VAL 417 (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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406A TRP* 3.4 19.0 - - + -
407A GLN* 4.0 0.9 - - - +
328B GLU* 6.2 1.3 - - + -
329B ILE 5.7 2.0 - - - +
330B GLN* 5.8 1.8 - - - +
390B LYS* 4.0 38.1 - - + +
391B LEU 3.1 22.5 + - - +
392B PRO* 3.6 15.9 - - + -
393B ILE 4.0 7.3 + - - +
415B GLU* 4.0 2.2 + - - +
416B PHE* 1.3 73.5 - - - +
418B ASN* 1.3 70.3 + - - +
419B THR* 3.7 6.1 - - - +
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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