Contacts of the strand formed by residues 208 - 214 (chain H) in PDB entry 5T0J
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 ILE 208 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47H ALA* 6.5 0.2 - - + -
48H THR 3.3 17.7 - - - +
49H GLU* 3.8 14.6 - - + -
50H LYS* 4.2 8.1 - - - +
203H MET* 5.0 20.6 - - + -
204H THR 4.1 13.0 - - - +
205H GLU* 3.2 21.3 - - - +
206H ASP 4.2 2.6 - - - -
207H ASN* 1.3 85.2 - - + +
209H GLU* 1.3 68.8 + - - +
210H VAL* 4.6 14.1 - - + -
223H PRO* 5.2 2.8 - - - +
226H VAL* 5.0 14.4 - - + +
231H ALA 5.7 4.7 - - - +
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Residues in contact with GLU 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H LEU 4.5 0.5 - - - +
47H ALA* 3.3 1.9 - - - -
48H THR* 2.7 52.3 + - + +
50H LYS* 5.9 3.4 - - + -
64H LYS* 6.4 0.4 - - + -
65H VAL* 3.3 29.0 - - + +
208H ILE* 1.3 80.2 - - - +
210H VAL* 1.3 84.2 + - - +
211H GLY* 3.4 9.8 + - - -
220H ARG* 4.2 16.4 - - - +
221H LEU* 3.5 28.5 + - - +
222H THR 5.6 0.9 - - - -
223H PRO* 5.4 11.7 - - + -
226H VAL* 5.4 4.7 - - + -
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Residues in contact with VAL 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 3.8 27.1 - - + -
46H LEU 3.2 4.5 - - - +
47H ALA* 3.8 15.9 - - + -
188H ILE* 6.1 1.3 - - + -
192H ILE* 5.5 11.0 - - + -
208H ILE* 4.6 14.6 - - + -
209H GLU* 1.3 92.2 - - - +
211H GLY* 1.3 62.6 + - - +
212H ILE* 4.5 5.6 - - + -
221H LEU* 3.3 32.1 - - + +
226H VAL* 5.1 10.9 - - + +
233H ILE* 5.5 9.4 - - + -
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Residues in contact with GLY 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 3.4 2.3 - - - +
46H LEU* 2.3 57.6 + - - +
65H VAL* 5.4 4.2 - - - +
75H VAL* 5.7 0.7 - - - -
209H GLU* 3.4 12.1 + - - -
210H VAL* 1.3 70.5 - - - +
212H ILE* 1.3 65.0 + - - +
218H PHE* 4.4 14.6 - - - -
219H ARG 4.7 3.1 - - - -
221H LEU 5.1 1.1 - - - -
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Residues in contact with ILE 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H VAL 3.4 4.9 - - - +
45H VAL* 3.7 28.0 - - + -
46H LEU* 6.0 0.4 - - - -
188H ILE* 6.0 0.4 - - + -
210H VAL* 4.5 7.4 - - + -
211H GLY* 1.3 79.5 - - - +
213H CYS* 1.3 59.3 + - - +
214H ASN* 3.8 18.1 + - - +
218H PHE* 3.1 19.4 - - - -
219H ARG* 3.2 36.0 + - + +
221H LEU* 4.0 31.9 - - + -
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Residues in contact with CYS 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H GLY* 3.2 9.5 - - - -
44H VAL* 2.4 52.7 + - + +
46H LEU* 5.4 1.3 - - - -
71H HIS 4.4 5.8 - - - +
73H GLY 3.7 8.1 - - - -
137H CYS* 3.5 33.0 - - + -
138H GLY* 4.2 13.0 - - - +
139H TRP* 6.0 0.4 - - + -
144H PRO* 5.6 0.5 - - - +
212H ILE* 1.3 70.3 - - - +
214H ASN* 1.3 65.6 + - - +
218H PHE* 3.4 31.2 - - - +
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Residues in contact with ASN 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H ASN 4.7 0.2 - - - -
43H GLY* 5.0 2.0 - - - -
71H HIS 4.9 0.9 - - - +
139H TRP* 4.0 10.5 - - - +
212H ILE* 3.8 20.9 + - - +
213H CYS* 1.3 79.0 - - - +
215H GLU* 1.3 60.6 + - - +
216H ALA* 3.0 14.3 - - + +
217H GLY* 3.0 38.7 + - - +
219H ARG* 4.4 21.2 - - - +
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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