Contacts of the helix formed by residues 213 - 221 (chain B) in PDB entry 3B60
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 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A HIS* 3.3 20.3 + - - -
429A PHE* 4.3 7.4 - - - -
209B GLN 2.7 20.1 + - - -
210B MET 3.7 0.4 - - - -
212B LYS* 1.3 72.5 - - - +
214B HIS* 1.3 64.1 + - - +
215B LYS 3.4 2.0 - - - -
216B GLU* 3.1 7.1 + - - +
217B VAL* 2.8 32.8 + - - +
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Residues in contact with HIS 214 (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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109A MET* 3.5 29.1 + - - +
112A PRO* 3.8 18.6 - - + +
113A VAL 4.3 6.6 + - - -
116A PHE* 3.2 51.4 - + + -
392A PHE* 6.3 0.9 - + - -
210B MET* 3.3 8.4 + - - +
211B LEU 2.9 17.4 + - - +
212B LYS 3.3 1.6 + - - +
213B GLY* 1.3 76.4 - - - +
215B LYS* 1.3 78.1 + - + +
217B VAL* 3.0 8.5 + - - +
218B LEU* 2.9 54.5 - - + +
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 5.7 6.3 - - - +
117A ASP* 4.9 11.3 + - - -
392A PHE* 4.0 38.8 - - + -
393A TYR* 5.4 10.1 - - - -
423A SER* 6.0 3.1 - - - +
212B LYS 5.7 2.7 - - - +
213B GLY 3.4 0.6 - - - -
214B HIS* 1.3 87.2 - - + +
216B GLU* 1.3 82.1 + - - +
218B LEU* 3.2 12.5 + - - +
219B ILE* 3.7 6.4 + - - +
479B VAL* 4.8 16.3 - - - +
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Residues in contact with GLU 216 (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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423A SER* 3.9 17.3 + - - -
427A HIS* 3.4 45.6 + - + +
429A PHE* 4.2 19.1 - - + -
493A ARG* 4.0 28.8 + - - +
497A ARG* 5.4 0.9 - - - +
212B LYS 4.4 1.0 - - - +
213B GLY* 3.1 10.0 + - - +
215B LYS* 1.3 88.8 - - - +
217B VAL* 1.3 53.0 + - - +
218B LEU 2.4 16.8 + - - -
219B ILE* 2.9 11.4 + - + +
220B PHE* 2.6 33.9 + - + +
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Residues in contact with VAL 217 (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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109A MET* 4.3 10.1 - - + -
429A PHE* 4.7 3.4 - - + -
209B GLN 5.2 0.7 - - - +
210B MET* 4.2 12.3 - - + +
213B GLY* 2.8 32.6 + - - +
214B HIS* 3.5 8.1 - - - +
216B GLU* 1.3 71.3 - - + +
218B LEU* 1.3 66.7 + - + +
220B PHE* 3.1 20.2 - - + +
222B GLY 4.3 0.4 - - - -
223B GLN* 3.4 48.4 + - + +
226B GLU* 4.0 26.7 - - + +
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Residues in contact with LEU 218 (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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109A MET* 5.0 4.0 - - + +
112A PRO* 4.8 7.2 - - + -
113A VAL 5.6 0.7 - - - +
392A PHE* 4.1 18.4 - - + -
416A ARG* 2.9 60.3 - - - +
214B HIS* 2.9 61.2 - - + +
215B LYS 3.6 6.3 - - - +
216B GLU 2.4 15.0 + - - -
217B VAL* 1.3 77.8 - - + +
219B ILE* 1.3 64.8 + - - +
220B PHE 3.1 1.1 + - - -
221B GLY* 3.6 8.5 + - - -
223B GLN* 4.5 11.1 + - + +
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Residues in contact with ILE 219 (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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390A THR* 4.6 18.6 - - + -
392A PHE* 3.9 28.9 - - + -
416A ARG* 3.9 28.3 - - + +
417A ASN* 5.4 1.2 - - - -
419A VAL* 4.7 11.0 - - + +
420A ALA* 5.4 0.2 - - - -
421A LEU* 3.5 40.2 - - + +
441A ARG* 4.3 3.6 - - - +
493A ARG* 5.7 3.1 - - - +
497A ARG* 3.9 27.1 + - - +
215B LYS 4.1 3.6 - - - +
216B GLU* 2.9 17.3 + - - +
218B LEU* 1.3 73.6 - - + +
220B PHE* 1.3 74.4 + - - +
221B GLY* 3.2 2.3 + - - -
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Residues in contact with PHE 220 (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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429A PHE* 2.8 37.2 - + - -
436A ASN 5.5 0.9 - - - -
439A TYR* 2.8 57.7 - + + -
441A ARG* 2.5 31.2 + - - +
443A GLU* 4.6 3.1 - - + -
493A ARG* 5.4 8.7 - - - -
497A ARG* 2.9 31.8 + - - +
216B GLU* 2.6 31.3 + - + +
217B VAL* 3.1 25.1 - - + -
219B ILE* 1.3 75.0 - - - +
221B GLY* 1.3 52.7 + - - +
222B GLY* 4.1 21.3 - - - -
225B VAL* 5.6 2.0 - - + -
226B GLU* 4.0 14.4 - - - -
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Residues in contact with GLY 221 (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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417A ASN* 6.5 1.1 - - - -
441A ARG* 2.4 58.3 + - - -
443A GLU* 3.8 3.4 - - - +
217B VAL 3.9 0.2 + - - -
218B LEU 3.6 8.2 + - - -
219B ILE 3.2 4.1 - - - -
220B PHE* 1.3 75.6 - - - +
222B GLY* 1.3 59.9 + - - +
223B GLN* 3.4 10.1 - - - -
224B GLU* 4.4 0.7 - - - +
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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