Contacts of the helix formed by residues 115 - 128 (chain A) in PDB entry 2AAT
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 GLY 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PMP 3.1 29.9 + - - -
114A GLY* 1.3 67.5 - - - -
116A THR* 1.3 58.4 - - - -
117A GLY 3.0 0.4 - - - -
118A ALA* 3.0 20.1 + - - +
119A LEU* 3.2 20.6 + - - +
223A ASP* 5.1 2.9 - - - -
225A ALA* 5.2 0.9 - - - -
253A ALA* 4.7 0.6 - - - +
254A SER 3.5 9.5 + - - -
255A SER* 3.2 16.7 - - - -
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Residues in contact with THR 116 (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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1A PMP 3.2 17.2 - - - +
2A SO4 5.3 2.9 - - - +
114A GLY 2.8 2.8 + - - +
115A GLY* 1.3 72.6 - - - -
117A GLY* 1.3 57.7 + - - +
118A ALA 3.3 2.0 + - - -
119A LEU* 3.9 7.8 + - - -
120A ARG* 3.7 17.7 + - - +
142A TRP* 3.0 44.0 - - + -
144A ASN* 3.8 17.8 + - - +
148A VAL* 4.0 11.2 - - - +
266A ARG* 5.7 2.9 - - - +
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Residues in contact with GLY 117 (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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112A THR* 3.6 6.4 + - - -
113A PRO* 3.3 24.6 - - - +
114A GLY 2.7 6.7 + - - -
116A THR* 1.3 79.2 + - - +
118A ALA* 1.3 59.2 - - - +
119A LEU 3.4 0.7 - - - -
120A ARG* 4.2 5.7 - - - +
121A VAL* 3.1 18.9 + - - +
266A ARG* 5.5 0.6 - - - +
294A ASN* 5.5 0.5 - - - +
295A TYR* 4.2 7.8 + - - -
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Residues in contact with ALA 118 (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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112A THR* 3.1 29.8 - - + +
114A GLY 4.0 0.8 + - - -
115A GLY 3.0 10.6 + - - +
117A GLY* 1.3 77.2 - - - +
119A LEU* 1.3 63.1 - - - +
121A VAL* 2.9 23.1 - - - +
122A ALA* 3.5 11.1 + - - +
253A ALA* 3.8 19.2 - - + +
254A SER 4.7 3.8 - - - +
269A ALA 4.2 1.8 - - - +
270A CYS* 3.8 18.3 - - + +
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Residues in contact with LEU 119 (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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1A PMP 4.6 0.2 - - + -
115A GLY 3.2 16.4 - - - +
116A THR* 4.1 3.4 - - - +
117A GLY 3.4 0.2 - - - -
118A ALA* 1.3 81.7 - - - +
120A ARG* 1.3 58.2 - - - +
121A VAL 3.3 0.4 - - - -
122A ALA* 3.0 23.1 - - - +
123A ALA* 3.5 7.6 + - - +
142A TRP* 3.7 17.9 - - + -
145A HIS* 2.8 39.0 - - + +
148A VAL* 3.8 15.8 - - + +
149A PHE* 4.2 13.8 - - + -
188A LEU* 5.5 0.4 - - + -
221A LEU* 4.9 7.6 - - + -
223A ASP* 3.8 26.5 - - + +
253A ALA* 3.2 32.8 - - + -
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Residues in contact with ARG 120 (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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116A THR 3.7 10.6 + - - +
117A GLY* 4.8 4.9 - - - +
118A ALA 3.3 0.6 - - - +
119A LEU* 1.3 77.7 - - - +
121A VAL* 1.3 49.1 + - - +
122A ALA 3.1 5.2 - - - -
123A ALA* 2.9 9.1 - - - +
124A ASP* 2.3 52.4 + - - +
148A VAL* 3.8 25.5 - - + +
151A SER* 3.1 39.6 + - - +
294A ASN* 4.3 21.6 - - - +
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Residues in contact with VAL 121 (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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112A THR* 3.5 9.0 - - - +
117A GLY 3.1 22.4 + - - +
118A ALA* 2.9 27.8 - - + +
120A ARG* 1.3 76.5 - - - +
122A ALA* 1.3 60.8 + - - +
123A ALA 3.4 0.2 - - - -
124A ASP* 3.7 4.7 - - - -
125A PHE* 3.4 22.5 + - - +
270A CYS* 4.6 8.3 - - + -
287A MET* 4.9 6.3 - - + +
290A ALA* 3.7 7.5 - - + +
291A ILE* 3.1 48.5 - - + +
294A ASN* 4.7 9.4 - - - +
295A TYR* 3.8 9.4 - - + +
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Residues in contact with ALA 122 (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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118A ALA 3.5 13.7 + - - +
119A LEU* 3.0 20.6 - - - +
121A VAL* 1.3 78.7 - - - +
123A ALA* 1.3 46.6 + - - +
125A PHE* 3.7 5.6 - - - +
126A LEU* 2.6 44.2 + - - +
149A PHE* 5.4 0.9 - - + -
221A LEU* 4.9 11.0 - - + -
251A ILE* 3.3 32.8 - - + -
270A CYS* 5.0 2.0 - - - -
287A MET* 6.2 0.7 - - - -
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Residues in contact with ALA 123 (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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119A LEU 3.5 3.6 + - - +
120A ARG* 2.9 24.0 - - + +
122A ALA* 1.3 74.4 - - - +
124A ASP* 1.3 58.9 + - - +
126A LEU* 3.6 4.1 - - - +
127A ALA 2.8 18.1 + - - -
148A VAL 3.8 18.8 - - - +
149A PHE* 4.8 13.4 - - + -
151A SER* 4.8 8.3 - - - -
152A ALA* 3.4 18.6 - - + +
154A LEU* 4.8 9.5 - - + +
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Residues in contact with ASP 124 (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 ARG* 2.3 48.3 + - - +
121A VAL* 3.7 6.0 - - - -
123A ALA* 1.3 69.7 - - - +
125A PHE* 1.3 62.8 + - - +
126A LEU 3.1 0.7 - - - -
127A ALA* 3.5 7.9 - - + +
128A LYS* 3.1 23.7 + - - +
152A ALA* 4.5 7.0 - - + -
290A ALA* 4.4 18.9 - - + +
294A ASN* 4.7 11.8 + - - +
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Residues in contact with PHE 125 (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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121A VAL 3.4 20.9 + - - +
122A ALA* 3.8 7.4 - - - +
124A ASP* 1.3 74.7 - - - +
126A LEU* 1.3 85.8 - - + +
128A LYS* 2.7 64.5 + - - +
129A ASN* 3.6 22.7 - - + -
130A THR* 4.2 2.7 - - - -
251A ILE* 5.2 10.3 - - + -
272A LEU* 3.8 22.7 - - + -
283A ALA* 3.2 29.8 - - + -
287A MET* 3.8 32.1 - - + +
290A ALA* 4.1 6.4 - - + +
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Residues in contact with LEU 126 (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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122A ALA 2.6 22.3 + - - +
123A ALA* 3.6 4.9 - - - +
125A PHE* 1.3 94.1 - - + +
127A ALA* 1.3 68.1 + - - +
128A LYS 2.9 6.8 - - - +
130A THR* 2.7 60.5 - - + +
132A VAL* 4.2 9.6 + - + +
149A PHE* 5.8 3.6 - - + -
154A LEU* 5.9 6.7 - - + -
186A VAL* 4.1 22.0 - - + -
219A LEU* 6.3 2.5 - - + -
221A LEU* 4.4 20.2 - - + -
251A ILE* 4.7 15.3 - - + -
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Residues in contact with ALA 127 (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 ALA 2.8 14.7 + - - +
124A ASP* 3.5 7.6 + - + +
125A PHE 3.3 0.8 - - - -
126A LEU* 1.3 68.9 - - - +
128A LYS* 1.3 67.7 - - - +
130A THR 2.7 13.2 - - - +
132A VAL 5.0 5.9 - - - +
152A ALA* 3.8 25.6 - - + -
154A LEU* 5.4 4.9 - - + -
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Residues in contact with LYS 128 (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 ASP 3.1 13.4 + - - +
125A PHE* 2.7 43.3 - - + +
126A LEU 2.9 1.9 - - - +
127A ALA* 1.3 90.3 - - - +
129A ASN* 1.3 90.7 - - - +
130A THR* 2.1 28.3 + - - +
283A ALA* 3.8 2.2 + - - +
286A GLN* 2.8 60.0 + - + +
290A ALA* 6.3 0.7 - - + -
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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