Contacts of the strand formed by residues 65 - 78 (chain A) in PDB entry 2ARE
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 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASP* 2.9 41.5 + - - +
59A TRP* 3.4 1.4 - - - +
60A GLU* 2.8 51.3 + - + +
63A SER* 2.8 30.3 + - - +
64A SER* 1.3 78.0 - - - +
66A VAL* 1.3 70.5 + - - +
204A ARG* 5.2 0.2 - - - -
237A LEU* 3.9 28.9 + - + +
238A LEU* 3.4 28.5 - - - +
239A TYR* 3.9 12.1 - - + +
10B THR* 5.9 1.4 + - - -
12B PRO* 5.8 2.0 - - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU 3.7 7.2 - - - +
59A TRP* 4.1 1.3 - - + -
64A SER 4.8 3.1 - - - +
65A ARG* 1.3 81.0 - - - +
67A ALA* 1.3 74.3 + - - +
176A PHE* 4.0 5.4 - - + -
178A PRO* 3.7 24.8 - - + +
202A ASP* 6.1 0.2 - - - +
203A VAL* 3.8 28.5 - - + -
204A ARG* 3.5 37.0 - - + +
237A LEU* 3.7 4.3 - - - -
238A LEU 3.1 24.1 + - - +
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Residues in contact with ALA 67 (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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57A HIS 3.8 15.7 - - - +
58A LEU* 2.8 32.4 + - + +
66A VAL* 1.3 75.4 - - - +
68A ASN* 1.3 65.4 + - - +
69A PHE* 3.9 2.9 + - + -
176A PHE* 3.4 26.2 - - - -
178A PRO* 3.8 2.3 - - - +
235A SER* 4.5 8.5 - - - -
236A THR 3.3 19.3 - - - +
237A LEU* 3.5 5.9 - - + +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL 3.7 1.0 + - - -
67A ALA* 1.3 73.6 - - - +
69A PHE* 1.3 68.3 + - - +
70A GLN* 5.4 1.9 - - - +
175A THR* 5.0 7.2 - - - +
176A PHE 3.4 17.6 + - - +
177A ASN* 4.0 12.7 - - - +
178A PRO* 3.6 17.1 - - + +
234A THR 4.0 0.2 - - - +
235A SER* 3.3 1.9 - - - -
236A THR* 2.9 32.9 + - - +
238A LEU* 3.8 23.1 - - + +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 6.5 0.4 - - + -
58A LEU* 4.0 29.2 - - + -
67A ALA* 4.4 3.4 - - + -
68A ASN* 1.3 78.9 + - - +
70A GLN* 1.3 66.0 + - - +
71A SER 4.8 0.7 - - - -
90A PHE* 4.6 5.8 - + - -
92A ILE* 3.5 31.0 - - + -
125A ILE* 6.2 0.4 - - + -
174A VAL* 4.5 11.9 - - + -
175A THR* 3.4 7.8 - - - +
176A PHE* 2.9 66.7 + + + -
183A LEU* 4.2 15.9 - - + -
203A VAL* 5.1 5.2 - - + -
233A PHE* 4.0 19.5 - + + -
234A THR* 3.1 12.6 - - - +
235A SER* 3.8 13.9 - - - -
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 5.4 2.0 - - - +
69A PHE* 1.3 76.5 - - - +
71A SER* 1.3 65.5 + - - +
72A GLN* 4.3 12.1 + - - +
173A LEU* 3.5 32.7 - - + +
174A VAL 3.3 6.5 - - - +
175A THR* 4.3 12.5 + - + +
232A SER* 4.0 2.9 + - - +
233A PHE* 3.4 5.8 - - - -
234A THR* 2.9 50.7 + - + +
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Residues in contact with SER 71 (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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69A PHE* 5.2 1.1 - - - -
70A GLN* 1.3 77.2 - - - +
72A GLN* 1.3 60.1 + - - +
73A PHE* 3.8 9.9 - - - -
90A PHE* 3.4 33.9 - - - -
172A VAL 3.8 1.0 - - - +
173A LEU* 3.6 1.4 - - - -
174A VAL* 2.8 40.0 + - - +
231A TRP* 3.0 26.3 + - - -
232A SER 3.3 4.3 - - - -
233A PHE* 3.9 7.4 - - - -
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Residues in contact with GLN 72 (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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70A GLN* 4.2 14.0 + - - +
71A SER* 1.3 75.1 - - - +
73A PHE* 1.3 67.9 + - - +
171A ASN* 6.1 4.1 - - + +
172A VAL 3.2 12.3 - - - +
173A LEU* 4.2 15.3 - - + +
231A TRP* 3.3 1.6 - - - -
232A SER* 2.8 50.4 + - - +
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Residues in contact with PHE 73 (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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71A SER* 3.8 15.3 - - - -
72A GLN* 1.3 82.4 - - - +
74A SER* 1.3 62.4 + - - +
75A PHE* 4.1 18.2 - + - -
88A ILE* 5.9 1.1 - - + -
90A PHE* 3.9 24.7 - + + -
129A PHE* 4.0 14.6 - + - -
171A ASN* 3.7 1.0 - - - +
172A VAL* 2.8 64.9 + - + +
174A VAL* 4.0 19.1 - - + -
215A PHE* 3.6 39.5 - + + -
228A LEU* 4.2 5.2 - - + -
230A SER* 3.2 19.1 - - - +
231A TRP* 4.1 2.5 - - + -
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Residues in contact with SER 74 (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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73A PHE* 1.3 76.5 - - - +
75A PHE* 1.3 65.1 + - - +
169A SER* 5.0 2.9 - - - -
170A LEU 3.1 7.2 - - - -
171A ASN* 3.4 24.2 - - - -
228A LEU* 3.7 5.5 - - - +
229A GLU* 2.9 43.9 + - - +
230A SER* 2.8 27.2 + - - -
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Residues in contact with PHE 75 (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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73A PHE* 4.1 17.3 - + - -
74A SER* 1.3 76.0 - - - +
76A SER* 1.3 65.2 + - - +
77A LEU* 3.9 29.2 - - + -
88A ILE* 3.7 33.7 - - + -
129A PHE* 3.6 39.7 - + + -
162A TRP* 4.3 6.3 - + - -
168A GLN 3.9 0.5 - - - +
169A SER* 3.3 1.9 - - - -
170A LEU* 2.9 60.3 + - + +
172A VAL* 4.0 7.6 - - + -
227A THR 3.0 19.7 - - - +
228A LEU* 4.2 3.1 - - + -
229A GLU* 3.9 6.0 + - - -
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Residues in contact with SER 76 (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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75A PHE* 1.3 77.7 - - - +
77A LEU* 1.3 66.8 + - - +
78A LYS* 4.3 4.5 + - - +
167A GLY* 4.4 12.3 - - - -
168A GLN 3.9 22.2 - - - -
169A SER* 4.1 1.6 - - - -
225A THR* 3.9 0.4 - - - +
227A THR* 3.0 43.4 + - - +
229A GLU* 2.9 22.0 + - - -
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Residues in contact with LEU 77 (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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75A PHE* 3.9 22.4 - - + -
76A SER* 1.3 82.1 - - - +
78A LYS* 1.3 56.9 + - - +
87A GLY* 5.6 0.4 - - - -
88A ILE* 4.5 4.0 - - + -
129A PHE 5.4 1.3 - - - +
131A THR* 3.7 30.3 - - + -
162A TRP* 4.0 17.0 - - + -
164A ARG* 4.0 12.1 - - + +
165A ARG 4.1 3.1 + - - +
166A ASP* 3.6 6.1 - - - -
167A GLY 2.7 31.1 + - - +
168A GLN 4.7 2.4 + - - -
224A GLN* 4.0 17.5 - - - +
225A THR 3.3 16.4 - - - +
226A HIS* 3.5 27.6 - - + +
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Residues in contact with LYS 78 (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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42A PRO* 4.0 4.9 - - + +
76A SER* 5.3 5.4 - - - +
77A LEU* 1.3 79.3 - - - +
79A SER* 1.3 64.8 + - - +
164A ARG* 3.8 0.9 - - - -
166A ASP* 3.4 9.4 - - - +
167A GLY* 3.7 20.2 - - - +
224A GLN* 3.2 1.0 - - - -
225A THR* 2.9 45.3 + - + +
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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