Contacts of the strand formed by residues 209 - 214 (chain A) in PDB entry 3D2I
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 LEU 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A GLU* 3.3 33.9 - - + +
195A VAL* 4.3 22.7 - - + +
198A GLN* 3.6 50.1 + - + +
199A SER* 4.9 2.6 + - - -
207A LEU 3.6 1.6 + - - -
208A ARG* 1.3 80.6 + - - +
210A TYR* 1.3 64.5 + - - +
211A GLY* 3.6 30.6 + - - +
221A LEU* 4.4 16.8 - - + -
222A ILE 3.7 4.7 - - - +
223A LEU* 3.8 20.9 - - + -
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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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141A TRP* 6.1 2.5 - - - +
170A PHE* 4.6 23.9 - + - -
172A LEU* 5.6 2.2 - - + -
208A ARG* 3.3 53.7 + - + +
209A LEU* 1.3 73.9 - - - +
211A GLY* 1.3 57.6 + - - +
222A ILE* 2.8 39.4 + - + +
223A LEU 4.0 2.7 - - - -
224A GLU* 3.7 36.9 - - - +
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 6.1 1.8 - - - -
195A VAL* 4.6 10.1 - - - -
209A LEU* 3.4 15.3 - - - +
210A TYR* 1.3 79.2 - - - +
212A TYR* 1.3 62.7 + - - +
222A ILE* 3.0 32.3 + - - +
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Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 5.9 1.7 - - - +
191A LEU* 4.6 13.9 - - + -
192A ARG* 3.6 31.2 + - + +
195A VAL* 3.9 34.5 - - + -
211A GLY* 1.3 74.8 - - - +
213A PHE* 1.3 69.1 + - - +
214A HIS* 5.8 6.5 - + - -
219A VAL* 3.6 28.5 - - + -
220A TYR 3.3 15.0 - - - +
221A LEU* 4.1 13.5 - - + -
222A ILE* 4.6 1.3 - - - +
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Residues in contact with PHE 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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141A TRP* 3.4 31.2 - - + +
142A THR* 3.6 4.7 - - + -
143A LEU* 3.3 34.1 - - + -
146A PHE* 3.7 24.9 - + - -
174A LEU* 4.1 4.3 - - + -
212A TYR* 1.3 76.0 - - - +
214A HIS* 1.3 69.1 + - - +
215A ASP* 6.3 0.2 - - + -
219A VAL* 3.7 3.8 - - - +
220A TYR* 2.8 71.9 + + + +
222A ILE* 3.6 35.2 - - + -
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Residues in contact with HIS 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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142A THR* 6.2 0.5 - - - +
212A TYR* 5.8 6.7 - + - -
213A PHE* 1.3 86.2 - - - +
215A ASP* 1.3 73.4 + - - +
216A ALA* 4.8 2.5 + - - +
218A ARG 3.3 17.5 - - - +
219A VAL* 4.2 16.2 - - + -
220A TYR* 4.5 1.8 - - - -
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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