Contacts of the strand formed by residues 39 - 46 (chain A) in PDB entry 1QAE
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 ALA 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.6 20.9 - - + -
31A ASN 3.3 13.2 - - - +
32A ASN* 3.9 6.4 + - - +
38A PHE* 1.3 73.6 - - - +
40A ASN* 1.3 64.6 + - - +
41A TRP 4.0 1.1 - - - +
42A VAL* 3.8 18.2 - - + -
90A GLN* 3.5 8.7 + - - +
109A SER 3.6 22.2 + - - +
112A THR* 5.3 0.2 - - - +
148A PRO* 3.2 22.3 - - - +
150A TYR* 4.4 0.8 + - - -
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Residues in contact with ASN 40 (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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17A GLY* 4.6 4.3 - - - -
18A SER* 2.9 33.5 + - - +
31A ASN* 2.7 30.8 + - - +
32A ASN 3.3 8.9 + - - -
33A ASN* 2.9 27.9 + - - +
38A PHE 3.6 0.2 + - - -
39A ALA* 1.3 72.8 - - - +
41A TRP* 1.3 73.6 + - + +
147A GLY* 3.8 3.3 - - - -
148A PRO* 3.4 19.1 - - - +
150A TYR* 5.2 7.3 - - - -
171A TRP* 3.9 6.9 - - - -
216A LEU* 4.1 9.7 - - + +
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Residues in contact with TRP 41 (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 CYS* 3.7 19.1 - - + -
14A PRO* 3.5 49.2 + - + +
17A GLY* 4.3 3.0 - - - -
22A SER* 3.7 25.4 - - - -
29A THR* 3.6 31.9 - - + -
30A LEU* 4.5 0.7 - - - -
31A ASN* 3.1 46.9 + - + +
39A ALA* 3.2 1.0 - - - +
40A ASN* 1.3 84.0 - - + +
42A VAL* 1.3 71.6 + - - +
43A ALA* 3.9 14.8 - - + -
145A VAL* 4.2 4.3 - - + -
146A THR 3.3 11.2 - - - +
147A GLY* 4.3 0.9 - - - -
171A TRP* 4.1 15.5 - - + -
216A LEU* 3.8 29.4 - - + +
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Residues in contact with VAL 42 (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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28A TYR* 3.8 29.2 - - + -
29A THR 3.4 5.8 - - - +
30A LEU* 4.2 8.3 - - + -
39A ALA* 3.8 20.0 - - + -
41A TRP* 1.3 81.7 - - - +
43A ALA* 1.3 63.6 + - - +
44A TYR* 4.1 1.7 - - + -
90A GLN* 3.8 22.7 - - + -
91A ALA* 3.8 21.3 - - + +
109A SER 5.1 0.4 - - - +
110A ASN* 3.9 7.2 - - - +
144A THR 3.9 0.7 - - - +
145A VAL* 3.4 1.8 - - - -
146A THR* 2.8 45.0 + - + +
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Residues in contact with ALA 43 (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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8A ASN* 3.8 8.5 - - - +
9A CYS* 3.6 31.6 - - - -
14A PRO* 5.1 0.2 - - + -
28A TYR* 3.3 4.3 - - - +
29A THR* 2.9 34.2 + - - +
41A TRP* 3.9 14.4 - - + -
42A VAL* 1.3 73.9 - - - +
44A TYR* 1.3 60.7 + - - +
144A THR 3.2 10.1 - - - +
145A VAL* 4.2 11.4 - - + +
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Residues in contact with TYR 44 (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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8A ASN* 3.7 10.5 + - - +
27A ALA 3.6 20.9 - - - +
28A TYR* 4.1 2.0 - - + -
42A VAL* 4.1 5.4 - - + -
43A ALA* 1.3 78.5 - - - +
45A HIS* 1.3 60.5 - - - +
46A ILE* 3.9 23.1 - - + -
91A ALA* 3.8 17.9 - - + -
92A PRO* 3.2 23.9 - - + +
96A LEU* 3.8 17.7 - - + -
130A GLU* 2.6 37.1 + - - -
142A VAL 3.8 0.2 - - - +
143A TYR* 3.6 2.8 - - - -
144A THR* 2.9 54.3 + - + +
146A THR* 4.0 13.7 - - + -
172A LYS* 3.2 17.7 + - - -
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Residues in contact with HIS 45 (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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7A ASP 4.5 6.1 + - - -
8A ASN* 4.0 19.6 + - - +
26A HIS 5.6 2.3 + - - +
27A ALA 4.9 0.8 + - - -
44A TYR* 1.3 76.0 - - - +
46A ILE* 1.3 71.3 + - - +
47A THR* 3.5 19.8 + - + +
50A THR* 3.9 9.0 - - - +
96A LEU* 3.7 11.5 - - - +
141A SER* 2.5 32.7 + - - -
142A VAL 3.5 7.6 - - - -
143A TYR* 3.2 44.2 + + + -
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Residues in contact with ILE 46 (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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44A TYR* 3.9 29.8 - - + -
45A HIS* 1.3 73.9 - - - +
47A THR* 1.3 68.8 + - - +
50A THR* 3.5 12.6 - - - +
51A PRO* 4.4 5.8 - - + -
95A SER* 3.7 28.3 - - - +
96A LEU* 4.1 9.2 - - + -
130A GLU* 4.0 26.2 - - + +
131A ARG* 4.7 5.2 - - - +
134A ILE* 3.7 20.5 - - + +
141A SER* 3.4 6.2 - - - -
142A VAL* 2.8 46.4 + - + +
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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