Contacts of the strand formed by residues 288 - 296 (chain A) in PDB entry 5B4N
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 ARG 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A GLN* 3.5 34.1 + - - +
171A TYR* 3.1 37.7 + - + -
172A PHE 3.2 12.6 - - - +
173A VAL* 4.0 15.0 - - + +
210A TYR* 3.1 6.4 - - - +
211A SER* 2.9 40.4 + - - +
212A GLY 3.1 24.2 + - - +
213A ARG* 3.9 20.2 - - + +
214A PRO* 4.6 11.6 - - - +
250A ALA* 4.5 9.3 + - - +
252A TRP* 3.6 10.3 - - + -
287A PRO* 1.3 75.8 - - - +
289A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 3.9 14.4 - - + -
171A TYR* 3.7 0.3 - - - -
172A PHE* 2.8 55.3 + - + +
181A LYS* 4.0 3.4 - - - +
209A TRP 3.3 7.0 - - - +
210A TYR* 4.0 3.8 - - + -
220A TYR* 3.8 24.7 - - + -
252A TRP* 3.9 2.9 - - - -
273A HIS* 3.3 44.4 - - + +
274A GLY* 5.0 2.7 - - - +
287A PRO* 4.3 9.2 - - + -
288A ARG* 1.3 79.5 - - - +
290A THR* 1.3 61.6 + - - +
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Residues in contact with THR 290 (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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131A PRO 4.0 6.7 - - - -
132A CYS* 3.4 14.9 - - - +
155A LEU* 5.0 0.2 - - + -
163A PHE* 3.5 37.0 - - + -
168A VAL* 4.0 4.3 - - + -
170A LYS 2.6 28.0 + - - +
171A TYR* 3.6 6.4 - - + -
172A PHE* 4.8 0.7 - - - -
208A ASP* 3.7 1.2 - - - +
209A TRP* 3.0 27.2 + - - +
252A TRP* 3.7 13.5 - - + -
289A VAL* 1.3 78.2 - - - +
291A ASN* 1.3 76.1 + - - +
292A SER* 3.2 5.9 + - - -
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Residues in contact with ASN 291 (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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126A ASN* 5.6 1.6 + - - -
131A PRO* 3.3 10.9 + - - +
132A CYS* 3.5 13.1 - - - -
163A PHE* 4.1 2.5 - - + -
164A PRO* 4.0 19.6 - - - +
165A ASN* 5.3 2.3 + - - +
168A VAL* 3.6 32.0 - - + +
207A LYS* 4.2 1.9 - - - +
209A TRP* 3.2 35.6 - - + +
290A THR* 1.3 86.0 + - + +
292A SER* 1.3 65.6 - - - +
293A SER* 3.2 10.0 + - - -
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 3.1 16.5 + - - -
128A LEU* 3.4 23.8 - - - +
131A PRO* 3.4 19.8 + - - +
140A TRP* 4.2 9.2 - - - -
181A LYS* 5.0 0.2 + - - -
207A LYS 3.6 3.4 - - - -
208A ASP* 2.6 26.4 + - - -
271A PHE* 3.6 9.2 - - - -
273A HIS* 3.4 16.6 + - - -
290A THR* 3.2 2.6 + - - -
291A ASN* 1.3 75.0 - - - +
293A SER* 1.3 58.6 + - - +
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Residues in contact with SER 293 (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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126A ASN* 3.2 23.1 - - - -
128A LEU* 3.8 2.8 - - - +
205A VAL 4.4 0.4 - - - -
206A VAL* 3.3 4.5 - - - +
207A LYS* 2.9 55.6 + - - +
271A PHE* 4.6 0.7 - - - -
291A ASN* 3.2 7.3 + - - -
292A SER* 1.3 74.4 - - - +
294A VAL* 1.3 64.4 + - - +
295A TRP* 3.5 29.1 - - - -
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Residues in contact with VAL 294 (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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126A ASN* 3.1 7.1 + - - +
127A LEU* 2.9 36.0 + - + +
128A LEU* 3.8 10.5 - - + +
185A ILE* 3.6 34.8 - - + -
187A LEU* 5.9 0.2 - - + -
204A ILE* 4.2 16.4 - - + -
205A VAL 3.4 4.0 - - - -
206A VAL* 3.8 23.1 - - + -
269A VAL* 4.2 14.1 - - + -
271A PHE* 4.0 14.1 - - + -
293A SER* 1.3 77.8 - - - +
295A TRP* 1.3 68.0 + - - +
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Residues in contact with TRP 295 (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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125A ARG 3.2 30.3 - - - +
126A ASN* 4.6 11.7 - - + -
127A LEU* 4.6 3.8 - - - -
204A ILE* 3.3 5.7 - - - +
205A VAL* 2.9 52.1 + - + +
207A LYS* 3.9 33.9 - - + -
293A SER* 3.5 32.3 - - - -
294A VAL* 1.3 78.6 - - - +
296A VAL* 1.3 68.6 + - - +
297A GLU* 3.1 32.4 + - - -
298A PRO* 6.0 0.4 - - + -
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Residues in contact with VAL 296 (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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127A LEU* 4.2 9.1 - - + +
187A LEU* 4.2 11.9 - - + -
192A TYR* 3.5 58.9 + - + -
197A LEU* 5.3 2.2 - - + -
202A PRO* 3.4 37.0 - - + +
203A ALA 3.3 4.9 - - - +
204A ILE* 4.3 13.2 - - + -
295A TRP* 1.3 83.2 - - - +
297A GLU* 1.3 67.3 + - - +
298A PRO* 3.7 6.8 - - - +
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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