Contacts of the helix formed by residues 53 - 68 (chain A) in PDB entry 1W4M
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 ASN 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.0 15.9 - - - +
52A ARG* 1.3 82.1 + - + +
54A ARG* 1.3 69.2 + - - +
55A GLN* 3.2 13.0 + - + +
56A GLU* 3.4 19.5 + - + +
57A GLY 3.3 12.5 + - - -
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Residues in contact with ARG 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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39A ASN* 4.0 21.9 + - - +
42A ILE* 3.3 23.2 - - + +
43A ASP* 4.9 10.3 + - - -
46A VAL* 4.1 9.8 - - + +
53A ASN* 1.3 78.6 + - - +
55A GLN* 1.3 58.6 + - - +
58A LEU* 3.0 36.3 + - + +
91A ASP* 5.3 7.4 - - - -
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Residues in contact with GLN 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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53A ASN* 3.2 9.9 + - + +
54A ARG* 1.3 78.2 - - - +
56A GLU* 1.3 65.5 + - + +
58A LEU* 3.2 11.1 + - + +
59A MET* 3.2 24.8 + - - +
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Residues in contact with GLU 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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50A SER 5.1 1.9 - - - +
51A VAL* 3.3 22.1 - - + +
52A ARG* 3.8 23.9 + - - +
53A ASN* 3.4 16.6 + - + +
54A ARG 3.3 0.2 - - - -
55A GLN* 1.3 81.7 - - + +
57A GLY* 1.3 59.0 + - - +
59A MET* 3.0 28.9 - - - +
60A ILE* 3.0 15.5 - - + +
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Residues in contact with GLY 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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42A ILE* 3.5 15.9 - - - +
45A LEU* 4.1 11.3 - - - +
51A VAL* 3.4 25.9 - - - +
53A ASN 3.3 8.8 + - - -
54A ARG 3.8 2.9 - - - -
55A GLN 3.3 0.2 - - - -
56A GLU* 1.3 79.2 - - - +
58A LEU* 1.3 60.4 + - - +
60A ILE 4.0 0.4 - - - -
61A ALA* 3.2 24.9 + - - +
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Residues in contact with LEU 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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42A ILE* 3.6 16.6 - - + -
54A ARG* 3.0 27.1 + - + +
55A GLN* 3.5 12.1 - - + +
56A GLU 3.1 0.4 - - - -
57A GLY* 1.3 76.9 - - - +
59A MET* 1.3 60.6 + - - +
61A ALA* 3.6 2.4 + - - +
62A SER* 3.0 28.7 + - - +
89A PHE* 4.5 19.1 - - + +
91A ASP* 3.6 46.9 - - + +
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Residues in contact with MET 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 GLN 3.2 11.1 + - - +
56A GLU* 3.0 27.4 - - - +
58A LEU* 1.3 76.8 - - - +
60A ILE* 1.3 88.6 + - + +
62A SER* 3.1 21.4 - - - -
63A SER* 3.2 9.0 + - - -
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Residues in contact with ILE 60 (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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6A LEU* 4.9 6.1 - - + -
9A LEU* 4.2 16.6 - - + -
45A LEU* 3.4 26.7 - - + -
50A SER* 4.4 4.9 - - - +
51A VAL* 3.7 15.9 - - + -
56A GLU 3.0 17.7 + - - +
57A GLY 4.1 0.2 - - - +
58A LEU 3.4 0.2 - - - -
59A MET* 1.3 100.0 - - + +
61A ALA* 1.3 59.4 + - - +
63A SER* 2.5 28.5 + - - +
64A LEU* 3.3 5.7 + - - +
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Residues in contact with ALA 61 (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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41A VAL* 3.9 17.7 - - + -
42A ILE* 4.0 1.3 - - + -
45A LEU* 4.6 0.6 - - + +
57A GLY 3.2 18.2 + - - +
58A LEU 3.9 2.0 - - - +
60A ILE* 1.3 77.6 - - - +
62A SER* 1.3 63.6 + - - +
64A LEU* 3.1 28.3 + - + +
65A LEU 3.3 1.9 + - - -
89A PHE* 3.3 46.3 - - + -
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Residues in contact with SER 62 (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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58A LEU* 3.0 16.7 + - - +
59A MET* 3.1 16.7 + - - -
61A ALA* 1.3 79.7 - - - +
63A SER* 1.3 62.3 + - - +
65A LEU* 3.5 3.5 + - - +
66A ASN* 3.0 22.3 + - - +
87A ASN* 5.7 1.0 - - - -
88A PRO* 4.4 12.9 - - - +
89A PHE* 3.5 28.3 + - - +
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Residues in contact with SER 63 (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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6A LEU* 3.0 32.1 - - - +
59A MET* 3.2 7.5 + - - -
60A ILE* 2.5 24.1 + - - +
62A SER* 1.3 76.1 - - - +
64A LEU* 1.3 71.9 + - - +
66A ASN* 2.7 21.5 + - - +
67A GLU* 2.8 15.5 + - - +
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Residues in contact with LEU 64 (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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6A LEU* 4.3 11.2 - - + -
9A LEU* 4.0 18.4 - - + -
10A TYR* 3.5 26.0 - - + -
13A MET* 3.8 26.5 - - + -
41A VAL* 4.8 2.5 - - + -
45A LEU* 4.9 0.9 - - + -
60A ILE 3.3 3.3 + - - +
61A ALA* 3.1 28.5 - - + +
63A SER* 1.3 83.7 + - - +
65A LEU* 1.3 61.2 + - - +
67A GLU 3.3 4.3 + - - -
69A TYR* 3.1 61.9 + - + +
70A LEU* 3.8 15.0 - - + -
89A PHE* 5.6 0.4 - - + -
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Residues in contact with LEU 65 (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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61A ALA 3.3 2.4 + - - -
62A SER 4.0 3.6 - - - +
63A SER 3.2 0.6 - - - -
64A LEU* 1.3 76.1 - - - +
66A ASN* 1.3 61.3 + - - +
68A GLY* 2.8 21.0 + - - -
70A LEU* 3.5 42.3 - - + +
72A PRO* 3.6 27.8 - - + -
81A VAL* 5.5 2.0 - - + -
88A PRO* 3.8 33.2 - - + +
89A PHE* 3.9 19.7 - - + +
97A TYR* 3.5 26.5 - - + -
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Residues in contact with ASN 66 (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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62A SER 3.0 15.5 + - - +
63A SER* 2.7 20.2 + - - +
65A LEU* 1.3 73.6 - - - +
67A GLU* 1.3 59.3 + - + +
68A GLY* 4.6 0.2 - - - -
88A PRO* 4.8 16.5 - - + +
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Residues in contact with GLU 67 (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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6A LEU* 3.1 31.2 - - + +
63A SER* 2.8 11.5 + - - +
64A LEU 3.6 9.6 - - - +
65A LEU 3.1 0.2 - - - -
66A ASN* 1.3 77.6 - - + +
68A GLY* 1.3 58.6 + - - +
69A TYR* 3.2 35.8 + - + -
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Residues in contact with GLY 68 (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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65A LEU* 2.8 14.0 + - - -
66A ASN 3.3 0.4 - - - -
67A GLU* 1.3 79.6 - - - +
69A TYR* 1.3 66.9 + - - +
70A LEU 3.4 10.8 - - - +
71A GLN* 4.2 8.2 + - - -
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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