Contacts of the strand formed by residues 205 - 210 (chain A) in PDB entry 3ELP
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 ILE 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.8 26.0 - - + -
100A LEU* 4.5 4.9 - - + -
183A ILE* 4.0 12.6 - - + -
184A LEU 3.2 2.9 + - - +
185A VAL* 3.4 34.0 - - + -
186A VAL 3.0 26.9 + - - +
199A LEU* 4.2 2.2 - - - -
203A ALA* 3.5 5.1 - - - +
204A ASP* 1.3 86.5 - - - +
206A SER* 1.3 65.2 + - - +
207A MET* 4.4 2.7 - - + +
225A VAL* 3.8 23.8 - - + -
226A SER 3.4 8.1 - - - +
227A VAL* 4.3 3.6 - - + -
232A LEU* 3.8 22.2 - - + -
236A LEU* 4.4 6.3 - - + -
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Residues in contact with SER 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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79A ASP* 4.2 18.3 + - - +
186A VAL 3.7 3.4 - - - -
188A ASN* 3.8 10.9 + - - +
198A PRO* 3.3 39.2 - - - +
199A LEU* 4.0 21.5 - - - +
205A ILE* 1.3 71.9 - - - +
207A MET* 1.3 59.9 + - - +
208A TYR* 4.0 0.7 + - - +
224A LEU 3.7 2.3 - - - +
226A SER* 3.1 31.1 + - - -
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLY* 3.4 14.6 - - - +
93A ALA* 4.2 7.2 - - + -
94A THR* 3.4 25.1 - - - +
97A ILE* 5.3 1.3 - - + -
155A TRP* 3.6 23.1 - - + -
185A VAL* 4.5 13.5 - - + -
186A VAL 2.9 13.8 + - - +
187A ASP* 3.5 18.2 - - - +
188A ASN* 2.9 30.5 + - - -
205A ILE* 3.9 4.9 + - + -
206A SER* 1.3 73.2 - - - +
208A TYR* 1.3 77.8 + - - +
209A SER* 3.7 16.6 - - - -
224A LEU 3.2 9.0 - - - +
225A VAL* 4.1 16.4 - - + +
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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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75A VAL* 5.8 2.0 - - + -
79A ASP* 5.3 8.5 - - - +
188A ASN* 4.3 4.5 - - + -
189A THR* 3.6 34.7 + - + -
192A SER* 4.1 20.5 - - - -
193A PRO* 4.1 27.4 - - + -
206A SER 4.0 0.8 + - - +
207A MET* 1.3 75.8 - - - +
209A SER* 1.3 65.8 + - - +
210A ALA* 3.9 23.7 + - + +
214A MET* 5.5 7.6 - - - +
222A MET 4.0 0.3 - - - +
224A LEU* 2.7 66.9 + - + +
255A CYS* 6.5 0.4 - - - -
259A LEU* 5.3 11.9 - - + -
262A LEU* 5.0 11.5 - - + +
266A MET* 5.9 0.3 - - - +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLY* 3.3 30.3 + - - -
187A ASP* 5.4 0.9 - - - -
189A THR* 2.8 42.7 + - - +
207A MET* 3.7 11.7 - - - -
208A TYR* 1.3 75.6 - - - +
210A ALA* 1.3 59.0 + - - +
211A THR* 3.9 10.9 + - - +
222A MET 3.6 5.2 - - - -
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Residues in contact with ALA 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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90A GLY 5.6 0.3 + - - -
208A TYR* 3.9 29.1 + - + +
209A SER* 1.3 73.4 - - - +
211A THR* 1.3 65.5 + - - +
214A MET* 6.3 3.4 - - + -
220A VAL 3.6 2.6 - - - +
221A VAL* 3.5 6.8 - - - +
222A MET* 3.0 43.5 + - + +
224A LEU* 6.0 2.0 - - + +
255A CYS* 5.7 5.8 - - - -
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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