Contacts of the strand formed by residues 215 - 225 (chain A) in PDB entry 1B70
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 VAL 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ARG* 3.3 34.8 - - + +
202A VAL 3.6 2.0 - - - -
203A PHE* 3.8 23.1 - - + -
213A GLU* 3.3 16.8 + - - +
214A ALA* 1.3 83.5 - - + +
216A PHE* 1.3 65.6 + - - +
320A GLU* 4.2 1.0 - - - +
336A PHE* 3.2 29.8 - - + -
513B TYR* 3.5 31.9 - - + -
514B SER 5.5 3.1 - - - +
515B PHE* 4.1 14.6 - - + -
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Residues in contact with PHE 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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201A ARG* 3.3 4.3 - - - +
202A VAL* 2.6 59.3 + - + +
204A ARG* 3.9 41.7 - - + -
206A GLU* 5.5 1.1 - - - -
213A GLU* 3.7 29.6 - - + -
214A ALA 3.8 11.0 - - - -
215A VAL* 1.3 82.2 - - - +
217A HIS* 1.3 73.0 + - - +
218A GLN* 4.5 11.0 - - + -
318A GLY* 5.8 4.0 - - - -
320A GLU* 3.1 25.6 - - + +
332A ILE* 5.4 2.5 - - + -
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Residues in contact with HIS 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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103A ILE* 4.1 27.2 - - + +
107A GLU* 5.1 8.1 - - - +
200A GLY* 3.4 9.9 - - - +
201A ARG* 3.5 40.6 + - + +
202A VAL* 4.8 0.2 - - - -
216A PHE* 1.3 79.4 - - - +
218A GLN* 1.3 66.6 + - - +
318A GLY* 4.0 0.7 - - - -
319A VAL* 3.2 34.8 + - + -
320A GLU* 2.9 28.9 + - - +
336A PHE* 4.0 25.6 - + - -
511B TYR* 4.1 17.1 - + - -
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Residues in contact with GLN 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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178A HIS* 3.3 10.3 - - - +
179A THR* 3.1 35.3 + - + +
198A VAL 3.7 1.0 - - - +
199A PRO* 3.5 2.8 - - - +
200A GLY 3.1 31.9 + - - +
202A VAL* 4.3 11.8 - - + +
204A ARG* 3.6 15.8 - - - +
216A PHE* 4.5 7.9 - - + -
217A HIS* 1.3 78.3 - - - +
219A LEU* 1.3 62.2 + - - +
220A GLU* 4.1 1.1 - - - +
316A GLY 5.7 0.8 - - - -
317A LEU 3.3 19.6 - - - +
318A GLY* 4.7 2.9 - - - +
319A VAL* 3.9 6.6 - - - +
352A PHE* 3.3 36.9 + - - +
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Residues in contact with LEU 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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110A LEU* 4.3 18.6 - - + -
111A VAL* 4.9 7.9 - - + -
114A PHE* 3.8 24.9 - - + -
179A THR* 4.3 0.9 - - - -
197A VAL* 3.6 34.3 - - + -
198A VAL 3.4 2.0 - - - -
199A PRO* 3.6 35.0 - - + -
218A GLN* 1.3 76.1 - - - +
220A GLU* 1.3 60.7 + - - +
315A PHE* 3.9 4.2 - - + +
316A GLY* 3.2 3.8 - - - -
317A LEU* 3.1 51.2 + - + +
319A VAL* 4.3 8.5 - - + -
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Residues in contact with GLU 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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179A THR* 2.8 27.4 + - - +
180A SER* 2.6 27.4 + - - -
183A GLN* 2.5 38.8 + - + +
197A VAL* 3.1 9.7 - - - +
198A VAL* 2.5 50.8 + - + +
218A GLN* 4.0 0.7 - - - +
219A LEU* 1.3 74.7 - - - +
221A GLY* 1.3 63.2 + - - +
222A LEU* 5.8 0.7 - - + -
315A PHE* 3.3 11.0 - - - +
316A GLY* 4.1 2.8 - - - -
352A PHE* 3.3 27.0 + - - -
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Residues in contact with GLY 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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119A TYR* 5.1 0.2 - - - -
196A ILE 3.5 9.0 - - - -
197A VAL* 4.2 1.1 - - - -
198A VAL* 6.1 0.2 - - - -
220A GLU* 1.3 77.4 - - - +
222A LEU* 1.3 61.4 + - - -
313A PHE* 5.8 0.2 - - - -
314A ALA* 2.9 9.0 - - - +
315A PHE* 2.6 63.5 + - - +
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Residues in contact with LEU 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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119A TYR* 4.7 0.4 - - - -
183A GLN* 3.8 32.1 - - + +
187A MET* 4.0 14.6 - - + -
194A PHE* 3.6 31.2 - - + +
195A ARG* 3.4 0.9 - - - -
196A ILE* 2.7 57.9 + - + +
220A GLU* 5.8 0.4 - - + -
221A GLY* 1.3 73.5 - - - +
223A VAL* 1.3 66.4 + - - +
224A VAL* 3.7 10.3 - - + -
286A VAL* 3.7 25.8 - - + -
313A PHE 3.5 17.0 - - - +
314A ALA* 3.8 6.5 - - + -
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Residues in contact with VAL 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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119A TYR* 3.2 46.7 - - + +
194A PHE 3.2 13.0 - - - +
195A ARG* 3.6 17.3 - - + +
222A LEU* 1.3 75.3 - - - +
224A VAL* 1.3 60.0 + - - +
228A ILE* 4.0 26.0 - - + +
312A GLY* 3.2 3.3 - - - -
313A PHE* 2.9 50.9 + - + -
477B PRO* 4.7 4.3 - - + -
479B PHE* 4.3 7.0 - - + -
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Residues in contact with VAL 224 (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 MET* 4.6 1.8 - - - -
192A PRO* 3.8 13.7 - - + -
193A PRO* 3.1 5.4 - - - +
194A PHE* 2.9 50.0 + - + +
222A LEU* 3.7 27.7 - - + -
223A VAL* 1.3 77.5 - - - +
225A GLY* 1.3 62.3 + - - +
228A ILE* 4.1 3.4 - - - -
291A PHE* 3.9 21.5 - - + -
307A TYR* 3.9 9.6 - - + -
310A VAL* 3.6 23.1 - - + -
311A THR 3.3 10.8 - - - +
312A GLY* 4.1 2.5 - - - -
479B PHE* 4.5 1.4 - - - -
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Residues in contact with GLY 225 (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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192A PRO* 4.5 4.3 - - - -
193A PRO* 3.9 16.8 - - - -
224A VAL* 1.3 79.8 - - - +
226A GLU* 1.3 67.3 + - - -
228A ILE* 3.0 23.6 + - - +
310A VAL* 4.2 1.3 - - - -
311A THR 2.9 22.4 + - - -
479B PHE* 5.8 0.9 - - - -
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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