Contacts of the strand formed by residues 207 - 212 (chain k) in PDB entry 5GJQ
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 207 (chain k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44k GLY* 3.1 3.9 - - - -
45k VAL* 3.0 53.0 + - + +
46k GLU 4.8 1.0 + - - -
62k ILE* 5.3 5.2 - - + -
205k ASN 4.3 0.2 - - - -
206k ILE* 1.3 77.1 - - - +
208k LEU* 1.3 61.5 + - - +
219k ILE* 5.2 11.2 - - + -
220k LEU 6.2 0.2 - - - -
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Residues in contact with LEU 208 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42k VAL* 5.9 2.5 - - + -
43k LEU 3.6 8.1 - - - +
44k GLY* 4.6 3.4 - - - -
188k ILE* 6.2 2.9 - - + +
191k VAL* 5.1 11.0 - - + -
192k ILE* 6.3 3.6 - - + +
206k ILE* 4.1 8.2 + - + -
207k GLU* 1.3 76.0 - - - +
209k ALA* 1.3 62.3 + - - +
210k VAL* 5.3 3.1 - - + -
219k ILE* 3.8 3.3 - - - +
220k LEU* 3.0 50.1 + - + +
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Residues in contact with ALA 209 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42k VAL* 3.5 0.9 - - - +
43k LEU* 2.9 32.1 + - + +
62k ILE* 4.0 28.9 - - + +
70k CYS* 6.0 1.1 - - - -
208k LEU* 1.3 75.2 - - - +
210k VAL* 1.3 68.6 + - - +
217k LEU* 3.8 20.0 - - + -
218k LYS 3.3 7.4 - - - +
219k ILE* 4.3 14.4 - - + -
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Residues in contact with VAL 210 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40k ILE* 5.6 5.8 - - + -
41k VAL 3.3 7.0 - - - +
42k VAL* 3.8 20.0 - - + -
188k ILE* 5.1 11.7 - - + -
208k LEU* 5.3 4.0 - - + -
209k ALA* 1.3 81.6 - - - +
211k MET* 1.3 65.9 + - - +
212k ARG* 6.1 1.6 - - + -
216k SER 4.2 0.9 - - - +
217k LEU* 3.4 5.7 - - - +
218k LYS* 2.8 60.5 + - + +
220k LEU* 5.2 13.5 - - + -
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Residues in contact with MET 211 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40k ILE* 3.4 4.7 - - - +
41k VAL* 2.9 50.1 + - + +
68k ASN 5.8 4.5 - - - +
70k CYS* 5.1 10.8 - - - -
134k VAL* 5.4 0.9 - - + -
135k GLY* 6.1 1.6 - - - -
136k PHE* 4.1 7.0 - - + -
210k VAL* 1.3 78.1 - - - +
212k ARG* 1.3 61.6 + - - +
213k ARG 5.5 0.7 - - - +
215k GLN 4.9 5.2 - - - +
216k SER 4.9 4.3 - - - -
217k LEU* 4.9 9.4 - - + +
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Residues in contact with ARG 212 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39k ASP* 3.1 19.5 - - + +
40k ILE* 4.5 5.4 - - + -
136k PHE* 4.0 1.3 - - - -
184k ASP* 4.9 7.6 - - - +
210k VAL* 6.1 2.5 - - + -
211k MET* 1.3 75.3 - - - +
213k ARG* 1.3 70.0 + - - +
215k GLN* 3.0 44.2 + - + +
216k SER 5.1 1.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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