Contacts of the strand formed by residues 207 - 212 (chain A) in PDB entry 3SAJ
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 GLY 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LYS 2.9 20.7 + - - -
179A GLU* 3.0 18.3 - - - +
180A ARG* 2.6 34.3 + - - +
206A ILE* 1.3 72.5 - - - +
208A TYR* 1.3 58.6 + - - -
231A ASN* 5.9 1.1 - - - -
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Residues in contact with TYR 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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171A PHE* 4.8 3.6 - - - -
174A LEU* 5.1 0.7 - - - +
180A ARG* 3.5 46.2 + - + -
182A VAL* 5.2 4.7 - - + -
198A ILE 5.8 0.4 - - - -
201A LEU 4.8 1.2 + - - -
202A GLU* 3.6 41.1 - - + +
203A LYS* 3.3 45.3 + - - +
206A ILE* 3.5 31.1 + - + +
207A GLY* 1.3 71.9 - - - -
209A HIS* 1.3 62.5 + - - +
210A TYR* 3.9 24.6 - + + -
231A ASN* 3.2 31.3 + - - +
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Residues in contact with HIS 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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122A TYR* 6.1 2.8 - + - -
124A TRP* 3.8 21.9 + + + -
179A GLU* 3.0 30.8 + - + +
180A ARG 2.9 12.4 + - - +
181A LEU* 4.0 16.6 - - + -
182A VAL* 2.7 34.1 + - - +
207A GLY 4.1 3.8 - - - -
208A TYR* 1.3 79.5 - - - +
210A TYR* 1.3 62.0 + - - +
231A ASN* 3.6 33.1 + - - +
354A LYS* 6.4 0.9 - - + -
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Residues in contact with TYR 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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182A VAL* 3.2 35.2 - - + +
184A VAL* 4.0 13.2 - - + -
195A LEU* 4.5 9.0 - - + -
198A ILE* 3.7 27.9 + - + -
199A VAL* 3.5 19.0 - - + +
202A GLU* 2.8 37.6 + - - +
208A TYR* 3.9 22.4 - + + -
209A HIS* 1.3 77.5 - - - +
211A ILE* 1.3 66.7 + - - +
212A LEU* 4.2 2.9 - - + -
230A ALA* 5.5 4.9 - - + -
231A ASN 3.0 22.1 + - - +
232A VAL* 3.3 21.1 - - + -
233A THR* 2.9 25.3 + - - -
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Residues in contact with ILE 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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115A LEU* 3.6 26.7 - - + -
118A ILE* 3.6 31.4 - - + +
119A ILE* 4.1 13.0 - - + -
122A TYR* 4.1 11.7 - - + -
124A TRP* 3.5 39.0 - - + -
182A VAL 2.8 10.2 + - - +
183A VAL* 3.3 7.3 - - + +
184A VAL 3.0 24.1 + - - -
210A TYR* 1.3 77.2 - - - +
212A LEU* 1.3 69.1 + - - +
213A ALA 3.5 0.7 + - - -
233A THR* 3.2 16.2 - - - +
234A GLY* 5.7 0.4 - - - -
235A PHE* 5.6 3.6 - - + -
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Residues in contact with LEU 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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184A VAL* 3.7 20.6 - - + +
191A LEU* 3.4 45.8 - - + -
195A LEU* 5.2 11.2 - - + -
210A TYR* 4.9 3.6 - - + -
211A ILE* 1.3 79.5 - - - +
213A ALA* 1.3 58.2 + - - +
214A ASN 3.1 19.2 + - - +
217A PHE* 3.8 27.4 - - + +
220A ILE* 5.5 0.7 - - + -
232A VAL* 3.9 22.4 - - + -
233A THR 2.8 13.5 + - - +
234A GLY* 4.1 15.4 - - - -
235A PHE* 4.1 10.6 - - - -
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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