Contacts of the strand formed by residues 275 - 284 (chain A) in PDB entry 2A1X
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.1 8.3 + - - +
161A LYS* 2.8 62.4 + - + +
193A TRP* 3.9 9.2 - - - -
197A GLU* 3.6 5.8 - - - +
199A ILE* 3.6 29.1 - - + +
203A ASN* 3.4 43.2 + - + +
204A GLY 2.9 29.2 + - - -
205A CYS* 4.9 0.6 - - - +
266A SER* 3.5 8.7 + - - -
269A ASN* 4.1 5.6 - - - +
273A GLY 4.8 0.2 - - - +
274A PHE* 1.3 71.3 - - - +
276A LYS* 1.3 59.2 + - - +
277A ALA* 3.8 18.8 - - - +
451A AKG 3.4 28.2 + - - -
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Residues in contact with LYS 276 (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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82A ARG* 4.3 27.1 - - + +
85A PHE* 3.9 25.9 - - + -
86A GLU* 5.3 8.0 + - - -
158A LEU* 4.5 7.2 - - + -
159A ILE 3.1 5.6 - - - +
160A ASN* 2.7 36.7 + - - +
196A MET* 3.2 41.1 + - + +
197A GLU* 2.9 20.0 + - - +
199A ILE* 3.8 10.0 - - - +
274A PHE* 4.0 13.3 + - - +
275A ARG* 1.3 73.7 - - - +
277A ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 277 (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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158A LEU* 3.5 3.6 - - - +
159A ILE* 2.7 38.5 + - + +
193A TRP* 3.4 45.1 - - + +
194A THR 3.3 15.3 - - - +
196A MET* 4.1 5.2 - - - +
199A ILE* 4.5 0.4 - - + -
275A ARG* 3.8 6.2 + - - +
276A LYS* 1.3 76.2 - - - +
278A ILE* 1.3 58.7 + - - +
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Residues in contact with ILE 278 (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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81A PHE* 4.1 32.1 - - + -
124A PHE* 3.8 24.7 - - + -
130A LEU* 4.2 8.3 - - + +
133A TYR* 3.9 38.1 + - + -
157A MET 3.5 10.3 - - - +
158A LEU* 4.0 20.2 - - + +
159A ILE* 5.3 0.2 - - - -
193A TRP* 3.6 0.9 - - - -
194A THR* 2.8 41.3 + - + +
196A MET* 4.0 14.7 - - + -
277A ALA* 1.3 74.6 - - - +
279A SER* 1.3 66.0 + - - +
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Residues in contact with SER 279 (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 PHE* 4.2 3.6 - - - -
133A TYR* 3.9 5.8 - - - -
155A HIS 4.1 0.2 - - - +
156A THR* 3.6 2.4 - - - -
157A MET* 2.7 74.0 + - - +
159A ILE* 4.7 1.3 - - - +
191A CYS* 4.5 5.2 - - - -
192A ALA 3.1 12.8 - - - -
193A TRP* 3.7 24.5 - - - -
278A ILE* 1.3 78.1 - - - +
280A CYS* 1.3 61.3 + - - +
281A HIS* 5.0 1.0 - - - -
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Residues in contact with CYS 280 (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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133A TYR* 3.8 20.0 - - + -
134A CYS* 4.0 11.0 - - - -
153A ALA* 3.9 14.8 - - - -
154A MET 4.5 0.2 - - - -
155A HIS 3.1 11.4 - - - +
156A THR* 4.3 4.5 - - + -
190A VAL 3.7 1.0 - - - +
191A CYS* 3.4 1.2 - - - -
192A ALA* 2.7 39.3 + - - +
279A SER* 1.3 75.1 - - - +
281A HIS* 1.3 73.8 + - - +
282A PHE* 3.5 35.5 - - + -
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Residues in contact with HIS 281 (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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154A MET* 2.9 30.0 + - + +
155A HIS* 2.9 35.6 + + + +
157A MET* 4.4 16.1 - - + +
177A ASP* 2.8 34.0 + - + +
181A PHE* 3.4 39.2 - + + -
183A PHE* 6.1 0.9 - - + -
189A ILE* 4.9 5.8 - - + -
190A VAL 3.2 5.6 - - - +
191A CYS* 3.4 34.1 - - + +
260A PRO* 5.8 3.1 - - + -
279A SER* 5.0 0.4 + - - -
280A CYS* 1.3 74.3 - - - +
282A PHE* 1.3 63.9 + - - +
451A AKG 5.5 0.7 - - - -
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Residues in contact with PHE 282 (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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133A TYR* 4.8 1.3 - + - -
134A CYS* 3.7 25.6 - - - -
139A ILE* 3.7 17.0 - - + -
140A LEU* 4.3 5.2 - - + -
143A VAL* 3.5 42.8 - - + -
147A THR* 4.2 1.1 - - + -
151A ILE* 4.1 14.6 - - + -
152A MET 3.2 8.1 - - - +
153A ALA* 3.8 17.9 - - + -
189A ILE* 3.2 7.5 - - - +
190A VAL* 2.7 42.0 + - + +
192A ALA* 3.7 20.9 - - + -
280A CYS* 3.5 33.4 - - + -
281A HIS* 1.3 75.0 - - - +
283A ALA* 1.3 60.9 + - - +
331A VAL* 4.7 1.6 - - + -
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Residues in contact with ALA 283 (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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147A THR* 4.1 5.8 - - - -
152A MET* 2.9 32.3 + - - +
154A MET* 3.7 20.6 - - + +
183A PHE* 4.1 7.4 - - + -
188A LEU 3.3 6.5 - - - +
189A ILE* 3.9 18.2 - - + -
282A PHE* 1.3 77.3 - - - +
284A SER* 1.3 65.7 + - - +
287A CYS* 4.1 2.7 - - - -
338A LEU* 3.9 13.2 - - + -
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Residues in contact with SER 284 (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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147A THR* 3.2 29.2 + - - -
150A ASN* 3.5 12.7 + - - +
188A LEU* 2.9 35.3 + - - +
283A ALA* 1.3 72.6 - - - +
285A ALA* 1.3 60.6 + - - +
286A ASP* 3.0 23.5 + - - +
287A CYS* 3.0 29.8 + - - +
338A LEU* 3.5 3.1 - - - +
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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