Contacts of the helix formed by residues 552 - 561 (chain B) in PDB entry 3HS5
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 GLY 552 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 3.5 18.8 - - - -
547B PRO* 2.8 26.8 + - - +
548B SER* 4.5 0.4 - - - -
551B GLY* 1.3 79.6 - - - +
553B GLU* 1.3 66.3 + - - -
554B VAL 3.3 3.0 + - - -
555B GLY* 3.4 2.3 + - - -
556B PHE* 3.1 18.7 + - - +
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Residues in contact with GLU 553 (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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5A EDO 3.5 20.6 + - - -
56A LYS* 6.1 0.2 - - - -
547B PRO* 3.6 23.2 - - - +
552B GLY* 1.3 72.1 - - - -
554B VAL* 1.3 59.6 + - + +
556B PHE* 3.6 16.5 + - - +
557B LYS* 3.0 30.6 + - + +
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Residues in contact with VAL 554 (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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315B ILE* 3.7 29.4 - - + -
316B LEU* 6.4 0.2 - - + -
319B GLU* 3.8 35.2 - - + +
551B GLY 5.4 0.9 + - - +
552B GLY 3.3 0.6 - - - -
553B GLU* 1.3 79.7 - - + +
555B GLY* 1.3 61.9 + - - +
557B LYS* 3.2 6.7 + - - +
558B ILE* 3.2 25.8 + - + +
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Residues in contact with GLY 555 (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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316B LEU* 4.8 5.8 - - - +
335B ILE* 3.8 22.3 - - - +
550B PHE* 3.4 25.1 + - - -
551B GLY 5.1 1.8 + - - -
552B GLY* 3.4 4.0 + - - -
554B VAL* 1.3 78.5 - - - +
556B PHE* 1.3 62.2 + - - +
558B ILE* 3.3 23.3 + - - +
559B ILE* 3.6 5.7 + - - +
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Residues in contact with PHE 556 (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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364B GLU* 6.1 0.7 - - - -
545B TRP* 3.5 52.7 - + - -
546B LYS 4.4 7.2 - - - -
547B PRO* 3.9 26.0 - - + -
550B PHE* 3.4 37.0 - + + +
552B GLY 3.1 17.5 + - - +
553B GLU* 3.7 24.9 - - - +
554B VAL 3.3 0.2 - - - -
555B GLY* 1.3 76.6 - - - +
557B LYS* 1.3 60.5 + - - +
559B ILE* 3.4 9.6 + - + +
560B ASN* 3.1 35.4 + - - +
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Residues in contact with LYS 557 (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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553B GLU* 3.0 20.0 + - + +
554B VAL* 3.2 6.9 + - - +
556B PHE* 1.3 74.3 - - - +
558B ILE* 1.3 58.3 + - - +
560B ASN* 4.4 5.6 - - + +
561B THR* 2.7 57.8 + - + +
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Residues in contact with ILE 558 (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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8B EDO 4.4 5.0 - - - +
308B GLU* 4.4 0.2 - - - +
311B ARG* 4.2 14.4 - - - +
312B VAL* 4.4 17.5 - - + -
315B ILE* 4.1 39.7 - - + -
316B LEU* 6.1 0.9 - - + -
335B ILE* 3.7 7.4 - - + -
339B GLU* 3.4 26.9 - - - +
554B VAL* 3.2 18.2 + - + +
555B GLY* 3.4 16.2 - - - +
556B PHE 3.3 0.4 - - - -
557B LYS* 1.3 76.0 - - - +
559B ILE* 1.3 62.7 + - - +
561B THR* 3.6 5.8 + - - -
562B ALA* 3.3 22.9 + - - +
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Residues in contact with ILE 559 (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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335B ILE* 3.4 26.7 - - + +
338B GLY* 3.6 27.4 - - - +
339B GLU* 4.3 7.2 - - - -
342B LYS* 3.3 22.3 - - - +
361B PHE* 4.1 6.7 - - + -
545B TRP* 3.8 25.6 - - + -
550B PHE* 3.5 51.6 - - + -
555B GLY 3.6 6.0 + - - +
556B PHE* 3.4 9.1 + - + +
557B LYS 3.3 0.2 - - - -
558B ILE* 1.3 76.9 - - - +
560B ASN* 1.3 60.7 + - - +
561B THR 3.2 4.9 + - - -
562B ALA* 3.3 5.2 + - - +
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Residues in contact with ASN 560 (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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342B LYS* 3.0 26.1 + - - +
361B PHE* 4.6 14.1 + - - -
545B TRP* 3.5 26.9 - - - -
556B PHE* 3.1 44.1 + - - +
557B LYS* 3.3 8.1 + - + +
559B ILE* 1.3 79.5 - - - +
561B THR* 1.3 62.9 + - + +
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Residues in contact with THR 561 (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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8B EDO 4.4 1.5 + - - -
342B LYS* 4.6 2.0 - - - +
557B LYS* 2.7 50.0 + - + +
558B ILE* 3.6 6.8 + - - -
560B ASN* 1.3 81.7 - - + +
562B ALA* 1.3 65.5 + - - +
563B SER* 3.7 4.5 + - - -
566B SER* 4.1 7.4 + - - -
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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