Contacts of the strand formed by residues 287 - 295 (chain A) in PDB entry 2E31
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 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLU* 4.1 5.3 + - - -
155A LEU* 5.8 0.2 - - - +
157A GLY* 3.2 24.9 - - - +
158A ASP 3.1 28.7 + - - +
160A GLY* 4.0 15.2 - - - -
161A VAL 5.7 0.6 + - - -
172A TYR* 3.2 48.7 + - + -
173A PHE 3.2 4.5 - - - -
174A ALA* 4.3 6.7 - - + +
211A TYR* 3.0 8.3 - - - +
212A SER* 2.7 54.8 + - - +
213A GLY* 4.2 11.1 + - - -
214A ARG* 3.5 29.1 - - - +
251A TRP* 3.5 9.6 - - + -
283A TRP 5.2 2.6 + - - -
285A GLY 4.1 5.9 + - - +
286A ALA* 1.3 74.6 - - - +
288A VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 288 (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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150A TRP* 3.5 32.5 - - + -
172A TYR* 4.4 0.9 - - - -
173A PHE* 2.9 40.5 + - + -
182A LYS* 4.1 1.6 - - - -
210A TRP 3.2 7.4 - - - +
211A TYR* 4.2 0.2 - - + -
221A TYR* 3.6 37.2 - - + -
272A HIS* 3.6 32.3 - - + +
273A GLY 4.8 4.7 - - - +
286A ALA* 5.1 2.7 - - + +
287A ARG* 1.3 79.8 - - - +
289A THR* 1.3 62.1 + - - +
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Residues in contact with THR 289 (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 3.6 7.2 - - - -
132A CYS* 3.3 16.0 - - - +
155A LEU* 5.5 0.9 - - + -
163A PHE* 3.9 20.4 - - + -
169A VAL* 3.8 8.4 - - + +
171A LYS 2.9 24.8 + - - +
172A TYR* 3.7 4.9 - - + -
173A PHE* 4.9 0.2 - - - -
209A ASP* 3.6 1.3 + - - +
210A TRP* 3.0 28.0 + - - +
251A TRP* 3.7 25.5 - - + -
288A VAL* 1.3 76.7 - - - +
290A ASN* 1.3 78.7 + - + +
291A SER* 3.2 6.4 + - - -
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Residues in contact with ASN 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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126A ASN* 5.9 0.3 + - - -
131A PRO* 3.0 11.1 + - - +
132A CYS* 3.6 11.3 - - - -
163A PHE* 3.7 15.4 - - + -
165A GLN* 6.2 0.2 - - - +
166A ASP* 4.8 9.1 + - - +
169A VAL* 3.8 23.3 - - + +
208A LYS* 4.2 3.3 - - - +
210A TRP* 3.3 37.4 - - + +
289A THR* 1.3 90.2 + - + +
291A SER* 1.3 63.7 + - - +
292A SER* 3.7 7.1 + - - -
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Residues in contact with SER 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* 3.0 16.8 + - - -
128A LEU* 3.7 20.2 - - - +
131A PRO* 3.1 20.5 + - - +
140A TRP* 4.2 7.8 - - - -
208A LYS 3.4 7.0 - - - -
209A ASP* 2.5 22.4 + - - -
270A PHE* 3.7 12.3 - - - -
272A HIS* 3.4 16.8 - - - -
289A THR* 3.2 4.0 + - - -
290A ASN* 1.3 76.3 - - - +
292A SER* 1.3 58.9 + - - +
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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
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126A ASN* 3.0 17.0 - - - -
128A LEU* 3.8 1.7 - - - +
206A VAL 4.4 1.0 + - - -
207A VAL* 3.5 1.4 - - - +
208A LYS* 2.9 53.9 + - - +
270A PHE* 4.7 0.2 - - - -
290A ASN* 3.7 5.3 + - - -
291A SER* 1.3 77.8 - - - +
293A VAL* 1.3 69.6 + - - +
294A TRP* 3.2 32.7 - - - -
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Residues in contact with VAL 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* 2.9 7.0 + - - -
127A LEU* 2.6 38.6 + - + +
128A LEU* 3.8 20.3 - - + +
186A ILE* 3.6 28.3 - - + -
188A LEU* 6.2 0.4 - - + -
205A ILE* 4.2 15.5 - - + -
206A VAL 3.4 8.7 - - - +
207A VAL* 3.8 21.3 - - + -
268A VAL* 4.3 9.6 - - + -
270A PHE* 3.9 14.1 - - + -
292A SER* 1.3 80.1 - - - +
294A TRP* 1.3 67.2 + - - +
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Residues in contact with TRP 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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124A ARG* 3.6 30.0 - - + +
125A ARG* 3.3 24.9 - - - +
126A ASN* 4.4 12.1 - - + -
127A LEU* 4.4 4.0 - - - -
204A ALA 3.8 0.2 - - - +
205A ILE* 3.6 2.8 - - - +
206A VAL* 2.8 53.3 + - + +
208A LYS* 3.6 30.7 - - + -
292A SER* 3.2 37.7 - - - -
293A VAL* 1.3 78.7 - - - +
295A VAL* 1.3 66.9 + - - +
296A GLU* 2.6 38.8 + - + -
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Residues in contact with VAL 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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120A LEU* 3.8 17.2 - - + +
124A ARG* 3.8 16.8 - - - +
127A LEU* 4.6 3.3 - - + +
188A LEU* 4.4 12.6 - - + -
193A TYR* 3.6 46.0 + - + -
198A LEU* 5.8 2.2 - - + -
203A PRO* 3.6 34.5 - - + +
204A ALA 3.3 7.4 - - - +
205A ILE* 4.2 18.2 - - + -
294A TRP* 1.3 76.2 - - - +
296A GLU* 1.3 63.1 + - - +
297A PRO* 3.8 6.2 - - - +
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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