Contacts of the strand formed by residues 132 - 138 (chain A) in PDB entry 3A4Y
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 LEU 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 27.8 - - + -
19A LEU* 3.6 24.2 - - + -
21A ALA* 4.0 26.9 - - + +
22A GLY* 5.1 4.5 - - - +
24A ARG* 5.2 2.7 - - + +
26A VAL* 4.2 15.5 - - + -
127A LEU 3.6 3.6 - - - +
128A ARG* 3.7 5.1 - - - -
129A LEU* 2.7 34.8 + - + +
131A ALA* 1.3 78.1 - - - +
133A SER* 1.3 61.6 + - - +
134A LEU* 3.3 21.3 - - + +
150A ALA* 4.5 4.3 - - + -
151A GLN 3.1 23.1 - - - +
152A GLY* 4.1 1.1 - - - -
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Residues in contact with SER 133 (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 TRP* 3.8 20.8 - - - -
127A LEU 3.6 4.5 - - - -
128A ARG* 4.0 5.0 - - - +
131A ALA 4.1 0.2 + - - -
132A LEU* 1.3 71.6 - - - +
134A LEU* 1.3 64.2 + - - +
149A VAL 3.6 0.9 - - - +
150A ALA* 3.3 4.3 - - - -
151A GLN* 2.7 52.7 + - - -
178D PRO* 3.8 4.2 - - - +
179D LEU* 2.9 40.1 + - - +
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Residues in contact with LEU 134 (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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19A LEU* 4.8 1.6 - - + -
26A VAL* 3.8 29.6 - - + -
28A LEU* 4.7 3.1 - - + -
56A LEU* 3.7 31.9 - - + -
121A LEU* 4.9 1.4 - - - +
125A GLU 3.6 1.0 - - - +
126A TRP* 3.3 7.7 - - - -
127A LEU* 2.8 51.2 + - + +
129A LEU* 5.3 7.0 - - + -
132A LEU* 3.3 35.7 - - + +
133A SER* 1.3 84.2 - - - +
135A ALA* 1.3 61.2 + - - +
148A VAL* 4.5 7.6 - - + -
149A VAL 3.3 3.8 - - - +
150A ALA* 4.0 13.7 - - + -
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Residues in contact with ALA 135 (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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56A LEU* 5.4 2.2 - - - +
121A LEU* 5.5 2.7 - - - -
124A GLY* 5.1 3.4 - - - -
125A GLU 3.9 14.1 - - - +
126A TRP* 3.4 37.9 - - + -
134A LEU* 1.3 75.7 - - - +
136A PHE* 1.3 67.4 + - - +
148A VAL* 3.6 3.9 - - - +
149A VAL* 2.8 44.0 + - + +
126D TRP* 5.9 2.5 - - + +
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Residues in contact with PHE 136 (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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56A LEU* 4.0 16.6 - - + -
57A LEU 3.3 34.5 - - - -
58A THR* 4.8 1.6 - - - -
81A TYR 4.2 1.8 - - - -
82A ALA* 3.7 21.8 - - - -
83A THR* 4.0 10.5 - - + -
121A LEU* 3.3 44.1 - - + +
122A GLU 4.5 1.1 - - - +
123A TYR* 3.7 17.7 - - + -
124A GLY* 3.3 21.1 + - - +
125A GLU 4.6 3.6 + - - -
135A ALA* 1.3 76.5 - - - +
137A GLY* 1.3 59.1 + - - +
146A ALA* 3.7 22.9 - - + -
147A PHE 3.4 7.0 - - - -
148A VAL* 3.8 23.6 - - + -
149A VAL* 5.6 0.9 - - - -
124D GLY* 4.0 6.1 - - - +
126D TRP* 5.5 1.3 + - - -
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Residues in contact with GLY 137 (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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123A TYR* 3.9 3.6 - - - -
135A ALA 4.0 0.2 + - - -
136A PHE* 1.3 73.7 - - - +
138A GLN* 1.3 63.2 + - - -
146A ALA* 3.1 6.2 - - - -
147A PHE* 2.8 55.9 + - - -
149A VAL* 5.5 0.2 - - - -
124D GLY 3.5 13.2 - - - -
126D TRP* 5.2 2.0 - - - -
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Residues in contact with GLN 138 (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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123A TYR* 3.7 37.5 + - + -
137A GLY* 1.3 67.6 - - - -
139A ALA* 1.3 63.4 + - - +
140A GLY* 3.1 24.5 + - - +
142A LEU 5.4 0.7 - - - +
145A SER* 3.6 8.1 + - - +
147A PHE* 3.3 9.8 - - - -
172A PRO* 3.4 29.7 - - + +
173A ASP 3.4 23.1 - - - +
174A PRO* 3.6 0.2 - - - +
175A SER* 2.8 37.9 + - - +
267A TYR* 5.4 2.0 + - - +
123D TYR 5.8 0.7 - - - +
124D GLY 3.8 6.6 + - - +
125D GLU* 4.5 21.4 + - + +
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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