Contacts of the helix formed by residues 46 - 59 (chain A) in PDB entry 1W5A
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A CYS* 1.3 72.6 - - - +
47A GLY* 1.3 56.1 + - - -
48A ALA 3.5 0.7 - - - -
50A ASN* 2.6 38.5 + - - -
69A ILE 3.1 11.7 + - - -
70A ASN* 3.4 18.8 - - - -
135A THR* 4.1 8.1 - - - +
500A GTP 3.4 21.3 - - - -
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Residues in contact with GLY 47 (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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46A GLY* 1.3 68.0 - - - -
48A ALA* 1.3 55.8 + - - +
50A ASN* 3.0 6.1 + - - +
51A ASN* 2.7 37.5 + - - +
70A ASN* 3.5 3.5 + - - -
75A GLN* 3.5 28.7 - - - -
500A GTP 2.8 20.3 + - - -
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Residues in contact with ALA 48 (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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47A GLY* 1.3 70.5 - - - +
49A GLY* 1.3 63.6 + - - +
51A ASN* 3.2 6.4 + - - +
52A THR* 3.0 27.2 + - - -
129A CYS* 4.6 1.1 - - - -
130A GLY* 3.8 15.7 - - - +
215A LEU* 5.3 3.5 - - + +
500A GTP 2.8 72.2 + - + +
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Residues in contact with GLY 49 (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 GLY* 3.6 7.9 - - - -
45A CYS 3.3 26.5 + - - -
46A GLY 3.3 2.6 + - - -
47A GLY 3.2 0.8 - - - -
48A ALA* 1.3 81.0 - - - +
50A ASN* 1.3 59.2 + - - +
52A THR* 3.2 8.2 + - - -
53A ILE* 3.1 26.0 + - - +
128A THR 3.8 11.9 - - - -
129A CYS* 3.9 6.0 - - - +
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Residues in contact with ASN 50 (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 GLY 3.4 9.2 - - - +
46A GLY 2.6 22.4 + - - +
47A GLY* 3.5 5.8 - - - +
49A GLY* 1.3 68.9 - - - +
51A ASN* 1.3 65.4 + - - +
53A ILE* 3.2 6.3 + - - +
54A THR* 3.0 27.5 + - - -
68A ALA* 3.5 13.8 - - - +
69A ILE 3.3 15.1 - - - +
70A ASN* 2.9 35.4 + - - +
75A GLN* 4.3 3.7 - - + +
76A LEU* 3.7 15.8 - - - +
79A THR* 3.2 24.8 + - + +
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Residues in contact with ASN 51 (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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47A GLY 2.7 20.2 + - - +
48A ALA* 3.6 6.9 + - - +
50A ASN* 1.3 72.5 - - - +
52A THR* 1.3 63.9 + - - +
54A THR* 3.6 10.5 - - - +
55A ARG* 3.4 25.3 + - - +
212A ASP* 2.9 40.6 + - - -
216A ILE* 6.3 0.2 - - - +
500A GTP 3.9 12.3 + - - +
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Residues in contact with THR 52 (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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48A ALA 3.0 14.5 + - - -
49A GLY* 3.4 10.2 - - - -
51A ASN* 1.3 77.6 + - - +
53A ILE* 1.3 65.4 + - - +
55A ARG* 3.2 8.0 + - - +
56A LEU* 3.1 43.6 + - + +
128A THR* 4.1 21.7 + - + +
129A CYS* 6.0 0.2 - - - -
212A ASP* 5.5 2.1 + - - -
215A LEU* 3.8 26.0 - - + +
216A ILE* 4.6 17.6 - - + +
219A VAL* 4.8 8.7 - - + -
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Residues in contact with ILE 53 (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 VAL* 3.6 35.0 - - + +
44A GLY* 3.5 29.2 - - - +
49A GLY 3.1 14.7 + - - +
50A ASN* 3.5 9.2 - - - +
52A THR* 1.3 77.1 - - - +
54A THR* 1.3 51.0 + - - +
56A LEU* 3.1 8.8 + - + +
57A LYS* 2.8 32.9 + - - +
66A THR* 3.8 13.8 - - + +
67A VAL 3.7 7.6 - - - +
68A ALA* 4.3 7.9 - - + -
79A THR* 4.7 0.2 - - + -
80A LYS 3.5 3.6 - - - +
81A ALA* 3.3 33.7 - - + -
128A THR* 4.9 1.6 - - + -
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Residues in contact with THR 54 (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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50A ASN 3.0 14.5 + - - -
51A ASN* 3.6 15.6 - - - +
52A THR 3.3 0.4 - - - -
53A ILE* 1.3 76.4 - - - +
55A ARG* 1.3 58.5 + - + +
57A LYS* 3.2 2.1 + - - +
58A MET* 2.8 56.9 + - + +
78A ARG 4.6 4.9 + - - +
79A THR* 3.5 8.0 + - - +
80A LYS* 3.3 38.2 + - + +
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Residues in contact with ARG 55 (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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51A ASN* 3.4 13.8 + - - +
52A THR 3.2 7.0 + - - +
54A THR* 1.3 77.2 - - + +
56A LEU* 1.3 62.7 + - - +
58A MET* 4.5 6.7 - - - +
59A GLU* 2.6 77.6 + - - +
209A LYS 5.3 0.4 + - - -
212A ASP* 5.1 5.8 - - + +
213A GLU* 2.5 44.5 + - - +
216A ILE* 3.0 43.0 - - + +
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Residues in contact with LEU 56 (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 VAL* 4.0 17.0 - - + -
52A THR* 3.1 27.9 + - + +
53A ILE* 3.5 10.3 - - + +
55A ARG* 1.3 76.6 - - - +
57A LYS* 1.3 58.3 + - - +
59A GLU* 3.7 1.9 - - - -
60A GLY 2.8 22.5 + - - -
61A ILE* 2.9 39.3 + - + +
66A THR* 4.4 4.3 - - + -
216A ILE* 4.2 20.4 - - + +
219A VAL* 3.9 23.6 - - + -
220A LYS* 4.0 33.7 - - + +
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Residues in contact with LYS 57 (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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53A ILE 2.8 10.1 + - - +
54A THR 3.6 2.0 - - - +
56A LEU* 1.3 78.4 - - - +
58A MET* 1.3 63.3 + - + +
60A GLY* 3.0 14.3 + - - -
61A ILE* 5.1 0.9 - - - +
66A THR* 3.7 17.4 - - + +
80A LYS* 3.4 37.2 - - + +
81A ALA 4.1 12.1 + - - +
82A ASP* 3.1 31.5 + - - +
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Residues in contact with MET 58 (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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54A THR* 2.8 45.0 + - + +
55A ARG* 4.0 6.7 - - - +
57A LYS* 1.3 74.3 - - + +
59A GLU* 1.3 62.6 + - + +
60A GLY* 3.2 1.2 + - - -
80A LYS* 4.3 26.9 - - + -
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Residues in contact with GLU 59 (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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55A ARG* 2.6 63.8 + - - +
56A LEU* 4.5 1.8 - - - +
58A MET* 1.3 75.5 - - + +
60A GLY* 1.3 65.4 + - - +
216A ILE* 5.0 6.1 - - - +
220A LYS* 3.9 28.7 + - + +
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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