Contacts of the strand formed by residues 10 - 14 (chain A) in PDB entry 2ADS
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 TYR 10 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 4.1 17.0 - - - -
9A LEU* 1.3 75.8 - - - +
11A ARG* 1.3 63.6 + - - +
12A ILE* 3.1 1.0 + - - +
154A LEU* 3.2 5.1 - - - -
155A LEU* 2.8 48.7 + - + +
156A HIS* 5.5 1.3 - - - -
157A LEU* 6.0 2.2 - - + -
284A LEU* 4.6 5.0 - - - +
287A ILE* 3.6 28.0 - - + +
288A ARG* 4.5 4.6 - - + +
291A LEU* 4.0 26.5 - - + -
305A ILE* 3.9 11.0 - - + -
306A SER 3.3 27.8 - - - +
307A PRO 3.9 6.7 - - - -
308A GLU 3.5 16.2 - - - -
309A GLU* 2.6 48.5 + - + +
310A GLU* 4.5 0.7 - - - -
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Residues in contact with ARG 11 (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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10A TYR* 1.3 67.7 - - - +
12A ILE* 1.3 60.3 + - - +
13A GLU* 4.6 11.0 - - - +
150A GLU* 2.8 42.7 + - - -
152A TYR* 3.3 52.6 + - + -
153A PHE 3.2 7.9 - - - +
154A LEU* 4.4 2.4 - - + +
304A TYR* 4.2 5.2 - - + +
305A ILE* 3.5 1.0 - - - -
306A SER* 2.8 46.5 + - - -
310A GLU* 3.3 24.2 + - - +
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Residues in contact with ILE 12 (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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10A TYR 3.1 0.4 + - - -
11A ARG* 1.3 74.7 - - - +
13A GLU* 1.3 72.7 + - - +
101A PHE* 5.6 2.9 - - + -
145A VAL* 5.5 5.6 - - + -
152A TYR* 5.6 0.5 - - - +
153A PHE* 2.7 53.4 + - + +
154A LEU 3.6 16.4 - - - +
155A LEU* 3.5 41.7 - - + -
303A TRP* 3.6 33.7 - - + -
304A TYR 3.4 12.8 - - - +
305A ILE* 4.2 8.7 - - + -
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Residues in contact with GLU 13 (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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11A ARG* 4.6 9.1 - - - +
12A ILE* 1.3 79.9 - - - +
14A TYR* 1.3 60.0 + - - +
15A ARG* 3.1 46.6 + - + +
152A TYR* 3.8 27.7 - - + -
153A PHE* 5.3 9.9 - - + -
302A GLY 4.1 1.1 - - - -
303A TRP* 3.2 10.2 - - - -
304A TYR* 2.8 60.9 + - + +
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Residues in contact with TYR 14 (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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13A GLU* 1.3 75.0 - - - +
15A ARG* 1.3 63.8 + - - +
16A PRO* 3.5 31.3 - - + +
88A PHE* 4.1 33.6 - + + +
89A ARG* 5.9 1.0 - - - -
90A GLY 5.5 5.0 + - - -
91A PHE* 5.8 4.9 - + + -
100A LEU* 5.2 0.4 - - + -
104A PHE* 3.6 36.4 - + - -
301A TYR* 3.4 38.6 + + - -
302A GLY* 3.6 16.2 - - - -
303A TRP* 3.5 45.8 - + + -
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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