Contacts of the strand formed by residues 210 - 215 (chain A) in PDB entry 1DRJ
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 MET 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A TYR* 4.9 2.9 - - - +
116A ILE* 3.5 26.5 - - + +
119A LYS* 3.4 31.2 - - - -
120A ALA* 3.4 24.9 - - + -
184A GLN 3.0 13.6 + - - +
185A ALA* 3.2 26.8 - - + +
186A VAL 2.7 32.9 + - - +
208A ASP 3.6 3.6 + - - +
209A VAL* 1.3 70.9 - - - +
211A VAL* 1.3 55.3 + - - +
212A VAL* 4.7 3.9 - - + +
230A ALA* 3.7 22.7 - - + -
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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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186A VAL* 3.5 25.4 - - + +
188A ALA* 4.9 0.4 - - + -
194A ALA* 4.1 27.8 - - + +
197A ALA* 4.8 3.6 - - + -
198A LEU* 3.9 21.8 - - + +
201A LEU* 3.5 32.8 - - + -
209A VAL 3.5 3.2 + - - +
210A MET* 1.3 77.6 - - - +
212A VAL* 1.3 65.8 - - - +
228A LYS 5.2 2.2 + - - +
229A LEU* 3.0 27.1 - - + +
230A ALA* 3.0 22.2 + - - +
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Residues in contact with VAL 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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112A ALA* 4.3 26.2 - - + +
115A TYR* 4.3 17.9 - - + -
116A ILE* 3.6 32.3 - - + -
186A VAL 2.9 11.6 + - - +
187A PHE* 3.7 3.0 - - + -
188A ALA* 2.9 30.5 + - - +
210A MET* 4.7 4.3 - - + -
211A VAL* 1.3 80.3 - - - +
213A GLY* 1.3 67.1 + - - +
229A LEU* 4.1 0.7 - - - -
230A ALA* 4.5 7.2 - - + -
231A ALA* 3.2 21.3 - - + +
232A THR 4.8 0.2 - - - +
233A ILE* 4.8 5.2 - - + -
267A LEU* 6.0 0.2 - - + -
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Residues in contact with GLY 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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187A PHE* 4.2 2.6 - - - -
188A ALA 3.5 10.2 - - - +
190A ASN 4.3 0.2 - - - -
191A ASP* 3.4 10.8 - - - -
194A ALA* 3.7 15.0 - - - -
212A VAL* 1.3 81.5 - - - +
214A PHE* 1.3 63.6 + - - +
229A LEU* 3.6 7.5 - - - +
231A ALA 2.8 11.1 + - - -
232A THR* 3.3 7.7 - - - -
233A ILE* 3.5 15.4 + - - +
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Residues in contact with PHE 214 (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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105A ASN* 4.2 8.3 - - - -
108A GLY* 3.5 39.7 - - - -
109A GLY 4.1 1.6 - - - -
141A ARG* 3.4 45.8 - - + -
187A PHE* 4.1 16.8 - + - -
188A ALA 3.9 1.3 - - - +
189A GLN 3.4 22.2 - - - +
190A ASN* 3.1 3.7 - - - -
191A ASP* 2.7 27.7 + - - -
213A GLY* 1.3 72.3 - - - +
215A ASP* 1.4 84.9 + - - +
232A THR* 3.3 7.0 - - - -
233A ILE* 3.6 27.1 - - + +
235A GLN* 3.8 19.7 - - + -
265A LEU* 4.4 5.4 - - + -
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Residues in contact with ASP 215 (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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13A ASN* 4.7 0.7 - - - +
15A PHE* 3.8 17.1 - - + +
190A ASN* 3.8 3.9 + - - +
191A ASP* 4.1 3.2 + - - +
192A GLU 5.5 0.2 + - - -
214A PHE* 1.4 81.6 - - - +
216A GLY* 1.3 62.4 + - - +
217A THR* 3.7 20.4 - - + +
233A ILE 2.8 19.8 + - - -
235A GLN* 2.8 46.8 + - - +
237A PRO* 5.0 3.6 - - - +
272A RIP 2.5 49.2 + - - -
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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