Contacts of the strand formed by residues 200 - 207 (chain E) in PDB entry 2JJD
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 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196E ASP* 3.6 1.5 - - - -
197E GLY 2.9 28.6 + - - +
198E TYR 3.1 7.8 + - - +
199E LYS* 1.3 80.0 - - - +
201E LYS* 1.3 72.1 + - - +
202E ASN 3.3 0.3 + - - +
203E LYS* 3.4 44.6 + - + +
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Residues in contact with LYS 201 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196E ASP* 3.5 13.7 - - - +
200E GLU* 1.3 78.2 - - - +
202E ASN* 1.3 76.7 + - - +
203E LYS 3.4 0.3 + - - -
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Residues in contact with ASN 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E TYR* 3.3 49.0 - - + +
195E ILE 3.7 6.1 - - - -
196E ASP* 2.8 26.5 + - - +
200E GLU* 3.3 0.8 + - - +
201E LYS* 1.3 79.9 - - + +
203E LYS* 1.3 65.2 + - - +
204E PHE 3.3 5.3 + - - -
330E PRO* 3.5 16.3 - - + +
373E GLN* 4.9 1.4 + - - -
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Residues in contact with LYS 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ILE 3.3 3.2 + - - -
197E GLY* 3.8 19.3 - - - +
198E TYR 5.4 0.7 - - - +
200E GLU* 3.4 42.3 + - + +
201E LYS 3.4 2.2 + - - -
202E ASN* 1.3 76.2 - - - +
204E PHE* 1.3 97.7 + - + +
330E PRO* 3.4 4.8 - - - +
331E ILE* 3.1 32.9 + - + +
349E ASP* 4.2 15.2 - - - +
350E ALA* 6.1 0.4 - - - +
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Residues in contact with PHE 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E TYR* 3.6 5.5 - - - +
195E ILE* 3.0 33.2 + - + +
196E ASP 4.3 1.8 - - - -
197E GLY* 4.3 7.4 - - - -
202E ASN 4.2 4.0 - - - -
203E LYS* 1.3 120.8 - - + +
205E ILE* 1.3 66.9 + - - +
330E PRO* 4.0 3.6 - - - +
331E ILE* 3.3 31.2 - - + +
333E VAL* 3.7 19.5 - - + -
345E PHE* 4.1 19.7 - + - -
346E ILE* 3.9 47.3 - - + -
349E ASP* 4.2 14.1 - - + -
350E ALA 5.7 0.4 - - - -
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Residues in contact with ILE 205 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176E VAL* 3.6 24.9 - - + -
192E ALA* 3.8 27.6 - - + -
193E SER 3.5 5.4 - - - +
194E TYR* 4.0 6.7 - - + -
204E PHE* 1.3 79.7 - - - +
206E ALA* 1.3 61.8 + - - +
207E ALA* 3.4 4.4 + - + -
221E MET* 4.0 17.5 - - + -
225E GLN* 3.8 21.1 - - + -
330E PRO* 3.7 26.7 - - + -
331E ILE 2.7 12.3 + - - +
332E VAL* 3.6 13.0 - - + -
333E VAL* 2.8 30.7 + - - +
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Residues in contact with ALA 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ALA* 3.3 1.9 - - - -
193E SER 2.9 29.5 + - - +
195E ILE* 3.6 30.6 - - + +
204E PHE* 4.1 1.8 - - - +
205E ILE* 1.3 69.4 - - - +
207E ALA* 1.3 59.0 + - - +
333E VAL 3.4 5.8 - - - -
338E GLY 3.8 18.4 - - - +
342E THR* 4.1 9.2 - - - +
346E ILE* 4.3 4.9 - - + -
374E ARG* 3.4 13.4 + - - -
377E MET* 4.2 3.6 - - + -
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Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ILE* 5.9 0.9 - - + -
191E ASN 3.7 0.7 - - - +
192E ALA* 3.5 22.9 - - + -
205E ILE* 3.4 8.9 + - + -
206E ALA* 1.3 74.6 - - - +
208E GLN* 1.3 66.5 + - - +
218E PHE* 4.6 3.4 - - + -
221E MET* 4.3 14.1 - - + -
332E VAL* 4.4 5.2 - - + -
333E VAL 3.0 10.5 + - - +
334E HIS* 3.0 30.0 - - + +
338E GLY* 3.5 11.4 + - - -
374E ARG* 4.4 0.4 - - - +
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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