Contacts of the strand formed by residues 35 - 39 (chain A) in PDB entry 1G6H
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 VAL 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP* 1.3 71.2 - - - +
36A THR* 1.3 58.9 + - - +
193A PHE* 4.2 6.5 - - + -
196A VAL* 3.8 22.7 - - + -
197A LEU* 4.3 5.8 - - + -
200A LYS* 4.1 20.6 - - + -
206A PHE* 3.9 8.5 - - + -
208A ILE* 4.2 21.8 - - + -
219A TYR 3.5 26.0 - - - +
220A ILE* 3.8 19.5 - - + +
221A ASP* 2.9 35.0 + - - +
222A HIS 3.2 6.1 + - - +
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 5.8 0.2 - - + -
30A VAL* 3.5 26.7 - - + +
34A ASP* 3.7 12.6 - - - +
35A VAL* 1.3 72.3 - - - +
37A LEU* 1.3 64.4 + - - +
38A ILE* 4.9 0.2 - - + -
206A PHE 2.9 15.1 + - - +
207A LEU* 3.9 21.1 - - + -
208A ILE* 2.8 30.9 + - - +
222A HIS* 3.3 22.6 + - + +
224A TYR* 4.1 27.4 - - + -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL 4.0 0.4 + - - -
36A THR* 1.3 75.6 - - - +
38A ILE* 1.3 62.8 + - - +
39A ILE* 3.5 24.2 - - + -
193A PHE* 5.0 3.4 - - + -
208A ILE* 3.2 34.8 - - + +
210A GLU* 3.8 23.8 - - + +
213A LEU* 3.6 39.7 - - + -
216A VAL* 5.4 1.1 - - + -
220A ILE* 3.8 28.7 - - + -
222A HIS 2.9 6.5 + - - +
223A LEU* 3.4 7.6 - - + +
224A TYR* 3.0 24.1 + - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.3 10.3 - - + -
37A LEU* 1.3 77.5 - - - +
39A ILE* 1.3 63.6 + - - +
46A LYS* 4.1 9.0 - - + -
49A LEU* 3.6 27.6 - - + -
50A ILE* 3.9 16.8 - - + -
207A LEU* 3.9 21.3 - - + -
208A ILE 2.8 10.7 + - - +
209A ILE* 3.2 12.4 - - + +
210A GLU 3.1 22.5 + - - +
224A TYR* 3.3 22.2 - - + +
226A MET* 3.7 34.8 - - + -
231A ILE* 5.8 0.4 - - + -
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.5 30.1 - - + -
38A ILE* 1.3 76.1 - - - +
40A GLY* 1.3 59.7 + - - +
46A LYS* 3.5 8.3 - - - +
210A GLU 3.1 17.5 - - - +
211A HIS 3.5 4.7 - - - +
212A ARG* 3.9 11.2 - - - +
213A LEU 4.3 9.4 - - - +
223A LEU* 3.9 9.2 - - + -
224A TYR 2.9 14.3 + - - +
225A VAL* 3.2 19.0 - - + -
226A MET* 2.8 25.1 + - - +
245A LEU* 3.8 29.4 - - + -
250A VAL* 5.4 1.1 - - + -
254A TYR* 3.7 17.0 - - + +
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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
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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