Contacts of the strand formed by residues 213 - 222 (chain I) in PDB entry 2B4X
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 213 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I THR* 5.1 0.9 - - + -
146I LEU* 3.8 33.9 - - + -
147I PHE 3.1 20.2 - - - +
148I GLY* 3.6 12.8 - - - +
212I VAL* 1.3 78.5 - - - +
214I VAL* 1.3 64.9 + - - +
351I LEU* 4.2 12.6 - - + -
354I ILE* 6.5 0.9 - - + -
362I LEU* 4.0 20.9 - - + -
363I TYR 2.9 19.5 + - - +
364I VAL* 3.5 29.3 - - + -
365I SER* 2.5 36.1 + - - -
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Residues in contact with VAL 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I LEU* 3.8 3.9 - - - -
147I PHE* 2.6 50.7 + - + +
175I PHE* 4.9 2.9 - - + -
186I ILE* 5.2 6.5 - - + -
202I ILE* 4.1 26.2 - - + -
206I ALA 5.4 2.9 - - - +
207I ILE* 5.3 7.2 - - + -
211I THR* 3.4 28.0 - - + -
213I LEU* 1.3 81.0 - - - +
215I LEU* 1.3 65.3 + - - +
216I VAL* 3.9 1.4 + - + -
364I VAL* 4.8 0.2 - - - -
365I SER* 4.2 6.3 - - - -
366I ASP* 3.2 18.2 - - + +
368I PHE* 4.1 10.5 - - + -
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Residues in contact with LEU 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ALA* 3.7 16.6 - - + +
87I PHE* 3.5 42.2 - - + +
89I MET* 5.5 4.0 - - - -
90I THR* 3.6 20.6 - - + +
145I ARG 3.4 21.8 - - - +
146I LEU* 3.4 25.8 - - + -
214I VAL* 1.3 74.0 - - - +
216I VAL* 1.3 59.3 + - - +
217I ASN* 3.8 9.1 + - - +
364I VAL* 4.7 9.0 - - + +
366I ASP 2.9 9.7 + - - +
367I ALA* 3.3 10.4 - - + -
368I PHE 2.8 32.2 + - - +
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Residues in contact with VAL 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ALA 4.7 0.9 - - - +
144I ASN* 3.5 1.7 - - - +
145I ARG 3.0 37.1 + - - +
147I PHE* 4.0 21.3 - - + -
186I ILE* 4.1 2.9 - - + -
189I TRP* 4.4 8.1 - - + -
190I VAL* 3.7 24.7 - - + -
201I VAL* 3.3 29.2 - - + -
202I ILE* 3.4 28.3 - - + -
214I VAL* 3.9 1.2 + - + +
215I LEU* 1.3 72.0 - - - +
217I ASN* 1.3 61.5 + - - +
368I PHE 3.4 8.1 - - - +
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Residues in contact with ASN 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I SER* 3.3 7.0 - - - +
83I ILE* 3.7 15.6 - - - +
86I ALA* 3.6 28.5 - - + +
87I PHE* 4.2 0.4 - - - -
143I ALA 3.5 2.0 - - - -
144I ASN* 2.8 19.3 - - - +
201I VAL* 5.6 1.7 - - - +
215I LEU* 3.8 15.0 + - - +
216I VAL* 1.3 78.4 - - - +
218I THR* 1.3 61.2 + - - +
331I LEU* 3.7 13.2 - - - +
368I PHE 3.2 11.5 + - - +
369I HIS* 2.5 59.3 + - - +
370I LYS 3.7 0.7 + - - -
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Residues in contact with THR 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I SER* 3.0 10.4 + - - -
143I ALA* 2.9 55.2 + - + +
144I ASN* 3.1 2.0 + - - +
190I VAL* 3.6 25.1 - - + -
194I THR* 3.9 4.0 - - + -
198I ILE* 3.5 18.6 - - - +
201I VAL* 5.7 1.3 - - + -
217I ASN* 1.3 75.7 - - - +
219I ILE* 1.3 79.5 + - - +
369I HIS* 3.8 4.7 - - - -
370I LYS 2.9 22.4 + - - -
371I ALA* 5.0 0.3 - - - -
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Residues in contact with ILE 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I SER* 3.3 22.9 - - - +
81I LEU* 4.9 6.5 - - + -
82I SER* 3.7 18.4 - - - +
131I TYR* 3.7 24.7 - - + +
140I LEU* 4.4 17.9 - - + -
141I VAL 3.4 14.1 - - - +
142I SER* 4.3 7.0 - - - +
143I ALA* 5.8 0.4 - - - -
144I ASN* 5.1 1.6 - - - +
194I THR* 5.2 0.9 - - - -
198I ILE* 4.0 10.5 - - - +
218I THR* 1.3 96.5 + - - +
220I LEU* 1.3 77.4 + - - +
369I HIS* 4.9 0.8 - - - -
370I LYS 4.9 0.2 + - - -
371I ALA* 5.9 0.7 - - - +
372I PHE 5.6 2.3 + - - +
421I ILE* 4.5 5.8 - - + -
422I PHE* 3.4 39.0 - - + -
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Residues in contact with LEU 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I LYS 3.5 6.0 - - - +
140I LEU* 3.5 1.0 - - - -
141I VAL* 2.9 53.3 + - + +
143I ALA* 6.5 0.2 - - + -
193I LYS 4.7 1.6 - - - +
194I THR* 3.9 28.0 - - + +
195I GLU* 4.2 22.4 - - + +
197I ARG* 3.5 45.1 - - + +
198I ILE* 5.4 0.9 - - + -
219I ILE* 1.3 76.8 - - - +
221I PHE* 1.3 65.6 + - - +
222I LYS* 4.7 16.4 - - + -
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Residues in contact with PHE 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I SER* 4.6 7.6 - - - -
139I LYS 3.8 4.3 - - - -
140I LEU* 3.5 22.2 - - + -
197I ARG* 5.1 3.8 + - - -
219I ILE 4.1 1.8 + - - -
220I LEU* 1.3 80.5 - - - +
222I LYS* 1.3 75.0 + - - +
223I GLY* 4.0 8.7 - - - -
274I PHE* 3.4 43.5 - + + -
279I ILE* 3.3 35.9 - - + -
372I PHE 5.7 0.9 + - - +
373I LEU* 5.1 9.1 - - + +
380I SER* 3.5 24.6 + - - -
412I ILE* 4.1 13.2 - - + -
422I PHE* 3.5 27.8 - + + -
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Residues in contact with LYS 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I SER* 3.1 22.4 + - - +
139I LYS* 3.2 20.5 + - - +
195I GLU* 5.3 5.6 - - - +
197I ARG* 4.9 14.1 - - - +
220I LEU* 4.7 14.4 - - + -
221I PHE* 1.3 81.5 - - - +
223I GLY* 1.3 59.1 + - - +
380I SER* 4.1 5.4 - - - -
381I GLU* 3.6 27.8 - - + +
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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