Contacts of the strand formed by residues 214 - 223 (chain A) in PDB entry 5AVD
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 GLN 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A VAL* 3.9 32.6 - - + +
209A CYS 3.5 0.9 - - - +
210A LEU* 3.7 6.0 - - - +
211A VAL* 2.9 32.7 + - - +
212A ASN 4.5 3.8 - - - +
213A GLY* 1.3 78.3 - - - +
215A TYR* 1.3 71.5 + - - +
216A ALA* 3.7 4.6 + - - +
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Residues in contact with TYR 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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27A TRP* 4.0 24.5 - + + -
128A VAL* 3.7 17.2 + - - +
141A PRO* 4.9 3.7 - - - +
143A TYR* 3.6 30.1 - + - -
208A HIS* 3.8 31.4 - - + +
209A CYS 3.4 13.7 - - - -
210A LEU* 3.6 39.4 - - + +
213A GLY 5.9 0.2 - - - -
214A GLN* 1.3 79.1 - - - +
216A ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 216 (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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128A VAL* 3.1 28.5 - - + +
129A LEU 4.4 0.4 - - - +
130A PRO* 4.4 9.0 - - + -
208A HIS* 3.4 2.7 - - - -
209A CYS 2.8 31.3 + - - +
211A VAL* 5.8 2.5 - - + -
214A GLN* 3.7 5.4 + - - +
215A TYR* 1.3 75.6 - - - +
217A VAL* 1.3 62.1 + - - +
218A HIS* 3.3 26.0 + - + +
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Residues in contact with VAL 217 (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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29A SER* 4.3 6.5 - - - +
48A THR* 3.8 27.4 - - + +
56A MET* 4.0 12.1 - - + -
127A GLY* 4.4 7.4 - - - -
128A VAL 2.7 15.8 + - - +
129A LEU* 4.0 8.7 - - + +
130A PRO* 3.1 19.1 - - - +
206A PRO* 3.7 17.3 - - + -
207A LEU 3.4 3.8 - - - +
208A HIS* 3.9 21.3 - - - +
215A TYR 6.1 0.2 - - - -
216A ALA* 1.3 71.2 - - - +
218A HIS* 1.3 58.7 + - - +
219A GLY 3.5 22.7 - - - +
241A VAL* 3.5 10.0 - - - +
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Residues in contact with HIS 218 (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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130A PRO* 3.7 32.6 - - + +
134A THR* 3.9 20.9 + - + +
136A LEU* 3.6 38.7 - - + +
188A VAL* 4.0 10.5 - - + +
207A LEU* 2.9 7.4 + - + -
209A CYS* 3.8 24.9 - - + -
211A VAL* 4.0 14.3 - - + +
216A ALA* 3.3 31.3 + - + +
217A VAL* 1.3 73.4 - - - +
219A GLY* 1.3 57.1 + - - +
239A THR 3.7 1.0 - - - +
240A ARG* 3.7 8.0 - - + +
241A VAL* 3.0 23.7 + - - -
242A SER* 4.6 0.7 + - - -
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Residues in contact with GLY 219 (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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188A VAL* 5.2 0.7 - - - -
206A PRO* 3.4 7.8 - - - +
207A LEU* 3.0 35.6 + - - +
217A VAL* 3.5 8.6 - - - +
218A HIS* 1.3 79.9 - - - +
220A VAL* 1.3 64.7 + - - +
238A PHE* 3.8 14.8 - - - -
239A THR 3.3 8.3 - - - -
241A VAL* 3.8 2.0 - - - -
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Residues in contact with VAL 220 (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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48A THR* 6.0 0.4 - - - +
56A MET* 3.9 28.7 - - + -
57A THR 3.6 29.6 - - - +
58A ALA* 3.6 12.1 - - + +
108A ASP 4.1 4.7 - - - +
109A ILE* 4.5 8.7 - - + -
204A GLY* 3.6 14.4 - - - +
205A GLY 3.3 3.8 - - - -
219A GLY* 1.3 75.0 - - - +
221A THR* 1.3 65.6 + - - +
222A SER 3.1 0.2 + - - -
238A PHE* 3.2 2.3 - - - -
239A THR* 2.8 44.2 + - - +
241A VAL* 3.8 17.3 - - + -
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Residues in contact with THR 221 (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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58A ALA* 3.8 7.1 - - - +
144A ILE* 3.8 9.7 - - + +
198A GLY* 5.3 1.6 - - - -
199A CYS 5.5 1.6 - - - +
202A ASP* 3.5 27.2 + - + +
203A SER* 3.5 20.9 - - - +
204A GLY* 2.8 25.1 + - - +
205A GLY 2.9 16.1 + - - -
220A VAL* 1.3 72.4 - - - +
222A SER* 1.3 63.7 + - - +
223A PHE* 4.9 1.3 - - - +
224A VAL* 6.0 1.3 - - + -
236A THR* 4.2 22.0 - - + -
238A PHE* 3.1 24.7 - - + -
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Residues in contact with SER 222 (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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60A HIS* 3.1 24.0 + - - -
103A VAL* 3.7 6.2 + - - +
108A ASP* 2.7 30.9 + - - +
187A MET* 6.0 0.8 - - - +
203A SER* 4.1 4.1 + - - -
220A VAL 3.1 6.9 + - - -
221A THR* 1.3 76.9 - - - +
223A PHE* 1.3 78.2 + - - +
237A VAL 2.8 16.3 + - - -
238A PHE 4.4 0.7 - - - -
239A THR* 4.0 16.4 - - - -
302A SO4 5.5 0.2 + - - -
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Residues in contact with PHE 223 (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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103A VAL* 3.8 30.1 - - + -
104A ALA* 5.0 0.4 - - - -
179A TRP* 3.6 34.5 - + - -
182A THR* 3.8 22.7 - - + -
183A VAL* 5.2 0.9 - - - -
187A MET* 4.1 21.1 - - + -
203A SER* 5.7 0.7 - - - -
221A THR* 4.9 2.3 - - - +
222A SER* 1.3 95.0 - - - +
224A VAL* 1.3 70.2 + - - +
236A THR* 4.1 1.2 - - - +
237A VAL* 2.9 70.3 + - + +
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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