Contacts of the helix formed by residues 204 - 213 (chain A) in PDB entry 6A5T
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 THR 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LYS* 6.3 0.7 - - - -
202A LEU* 3.1 23.3 + - + +
203A LEU* 1.3 76.0 - - - +
205A PRO* 1.3 74.8 - - - +
206A GLY 3.9 2.1 + - - -
207A GLU* 3.0 40.9 + - - +
208A ILE* 3.2 21.4 + - - +
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Residues in contact with PRO 205 (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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88A LYS* 3.3 29.8 - - - +
89A PRO* 3.4 23.1 - - - +
90A VAL* 4.8 0.9 - - - -
91A PHE* 4.4 33.0 - - + -
202A LEU* 5.6 5.6 - - + -
203A LEU 3.8 2.4 - - - +
204A THR* 1.3 88.0 - - - +
206A GLY* 1.3 64.1 + - - +
208A ILE* 3.4 3.2 + - + +
209A LEU* 2.9 23.2 + - - +
236A ILE* 4.9 9.4 - - + +
298A GLN* 4.9 6.5 - - - +
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Residues in contact with GLY 206 (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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88A LYS* 6.0 2.0 - - - +
89A PRO* 4.8 12.1 + - - -
204A THR* 3.4 2.4 + - - -
205A PRO* 1.3 81.0 - - - +
207A GLU* 1.3 63.0 + - - +
209A LEU* 3.0 8.7 + - - +
210A ASN* 3.0 30.0 + - - -
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Residues in contact with GLU 207 (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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108A MET 5.6 1.6 - - - +
201A LYS* 5.3 9.5 + - - -
202A LEU 5.3 0.7 - - - +
203A LEU* 5.5 1.3 - - - -
204A THR* 3.0 34.3 + - - +
206A GLY* 1.3 76.5 - - - +
208A ILE* 1.3 65.0 + - + +
209A LEU 3.1 0.3 + - - -
210A ASN* 3.3 6.9 + - - +
211A VAL* 2.9 34.3 + - + +
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Residues in contact with ILE 208 (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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91A PHE* 5.2 6.3 - - + -
99A ILE* 4.8 4.3 - - + -
103A CYS* 3.8 27.8 - - - -
108A MET* 6.3 3.1 - - + -
182A LEU* 4.5 14.6 - - + -
203A LEU* 3.5 41.5 - - + +
204A THR 3.2 19.3 + - - +
205A PRO* 3.9 2.9 - - + +
207A GLU* 1.3 77.7 - - + +
209A LEU* 1.3 56.9 + - - +
211A VAL* 3.4 9.8 - - + +
212A PHE* 2.9 47.0 + - + -
236A ILE* 5.0 7.0 - - + -
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Residues in contact with LEU 209 (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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89A PRO* 4.5 18.2 - - + -
205A PRO 2.9 15.3 + - - +
206A GLY* 3.0 11.6 + - - +
208A ILE* 1.3 74.5 - - - +
210A ASN* 1.3 67.2 + - - +
211A VAL 3.2 0.3 + - - -
212A PHE* 3.2 4.2 + - + +
213A LYS* 3.0 39.2 + - + +
233A GLU* 3.4 31.6 - - + +
236A ILE* 4.0 28.0 - - + +
238A THR* 4.5 18.6 - - + -
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Residues in contact with ASN 210 (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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206A GLY 3.0 17.1 + - - +
207A GLU* 3.9 8.4 - - - +
209A LEU* 1.3 77.1 - - - +
211A VAL* 1.3 64.2 + - + +
213A LYS* 3.3 25.6 + - - +
214A HIS* 3.3 33.2 + - + +
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Residues in contact with VAL 211 (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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106A ILE* 4.7 2.7 - - + -
107A CYS 4.4 10.5 - - - +
108A MET* 4.0 24.7 - - + +
109A ASN 5.6 2.7 - - - +
110A CYS 4.6 3.4 - - - +
111A GLY* 4.4 19.7 - - - +
207A GLU* 2.9 29.5 + - + +
208A ILE* 3.4 13.5 - - + +
209A LEU 3.1 0.4 - - - -
210A ASN* 1.3 78.3 - - + +
212A PHE* 1.3 76.4 + - + +
214A HIS* 3.2 23.2 + - - +
215A ILE* 4.2 5.7 - - - +
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Residues in contact with PHE 212 (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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99A ILE* 3.9 16.4 - - + -
102A VAL* 3.8 26.5 - - + -
103A CYS* 3.5 31.4 - - - -
106A ILE* 4.1 20.0 - - + -
208A ILE* 2.9 30.1 + - + +
209A LEU* 3.9 1.8 - - - +
211A VAL* 1.3 82.6 - - + +
213A LYS* 1.3 58.2 + - - +
214A HIS 2.7 7.8 + - - -
215A ILE* 3.4 25.0 + - + +
231A ARG* 4.3 0.3 + - - -
232A PRO* 2.8 24.9 - - + +
233A GLU* 3.3 32.5 - - + +
235A MET* 4.3 7.0 - - + -
236A ILE* 4.4 10.3 - - + -
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Residues in contact with LYS 213 (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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209A LEU* 3.0 35.7 + - + +
210A ASN* 3.6 23.4 + - - +
211A VAL 3.1 1.2 - - - -
212A PHE* 1.3 75.9 - - - +
214A HIS* 1.3 65.9 + - + +
215A ILE 3.6 0.9 - - - -
231A ARG* 4.5 6.4 + - - -
233A GLU* 3.8 28.0 - - + +
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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