Contacts of the helix formed by residues 52 - 67 (chain A) in PDB entry 3DRW
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 GLU 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.8 5.4 + - - -
50A ILE* 3.7 3.5 - - - +
51A ASN* 1.3 84.7 - - + +
53A PRO* 1.4 77.5 - - + +
54A ILE* 4.2 19.3 - - + +
55A ASP* 2.9 37.2 + - - +
56A PHE 3.5 2.3 + - - -
79A MET* 3.4 6.5 - - - -
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Residues in contact with PRO 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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34A PHE* 3.8 18.6 - - + -
52A GLU* 1.4 85.6 - - + +
54A ILE* 1.3 64.3 + - - +
56A PHE* 3.0 6.2 + - - +
57A VAL* 3.0 22.9 + - - +
79A MET* 3.4 21.3 - - + -
82A TRP* 3.7 48.5 - - + +
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Residues in contact with ILE 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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34A PHE* 3.7 31.6 - - + -
38A GLU* 4.3 9.6 - - + +
39A VAL* 3.7 36.6 - - + +
42A ARG* 4.0 28.7 - - + -
52A GLU* 4.2 24.4 - - + +
53A PRO* 1.3 79.7 - - - +
55A ASP* 1.3 54.6 + - - +
57A VAL* 4.4 3.4 - - + -
58A ALA* 2.8 32.6 + - - +
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Residues in contact with ASP 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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42A ARG* 2.6 45.5 + - - +
47A PRO* 4.0 11.4 - - + +
49A GLU 3.7 9.1 - - - +
50A ILE* 3.9 17.2 - - + +
51A ASN* 2.9 28.8 + - - +
52A GLU* 2.9 27.7 + - - +
54A ILE* 1.3 75.1 - - - +
56A PHE* 1.3 65.2 + - - +
58A ALA* 4.0 1.2 - - - +
59A ARG* 3.1 30.1 + - - +
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Residues in contact with PHE 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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30A LEU* 3.9 12.8 - - + -
50A ILE* 3.9 24.0 - - + +
52A GLU 3.5 1.2 + - - -
53A PRO 3.0 7.8 + - - +
55A ASP* 1.3 81.7 - - - +
57A VAL* 1.3 61.7 + - + +
59A ARG* 3.8 1.5 - - - +
60A LEU* 2.8 45.2 + - + +
79A MET* 4.6 2.7 - - + -
82A TRP* 3.7 18.8 - + - -
83A PHE* 3.8 16.6 - + + -
87A PHE* 3.6 24.2 - + - -
163A PHE* 3.7 40.8 - + - -
186A PHE* 3.7 28.7 - + - -
188A VAL* 3.8 5.6 - - + -
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Residues in contact with VAL 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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30A LEU* 3.9 20.9 - - + -
31A ILE* 3.5 30.1 - - + -
34A PHE* 3.5 38.8 - - + -
39A VAL* 4.3 13.0 - - + -
53A PRO 3.0 15.7 + - - +
54A ILE* 3.9 7.2 - - + +
56A PHE* 1.3 81.6 - - + +
58A ALA* 1.3 62.4 + - - +
60A LEU* 4.6 3.1 - - - -
61A VAL* 2.9 27.0 + - + +
82A TRP* 4.5 0.7 - - + -
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Residues in contact with ALA 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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39A VAL* 4.0 8.9 - - + +
42A ARG* 3.7 31.4 - - + +
43A ILE* 3.3 32.6 - - + +
47A PRO* 4.7 3.1 - - + -
54A ILE 2.8 22.3 + - - +
55A ASP 4.0 2.2 - - - +
57A VAL* 1.3 73.4 - - - +
59A ARG* 1.3 63.8 + - - +
62A HIS* 3.0 21.0 + - - +
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Residues in contact with ARG 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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43A ILE* 6.2 0.9 - - - +
46A TYR* 3.3 54.2 + - - -
47A PRO* 2.9 46.6 + - + +
48A ARG* 4.1 8.9 + - - +
55A ASP 3.1 20.2 + - - +
56A PHE* 5.0 0.4 - - - -
58A ALA* 1.3 74.6 - - - +
60A LEU* 1.3 66.2 + - - +
62A HIS* 3.4 9.8 + - - +
63A THR* 3.0 25.0 + - - -
70A ALA* 4.1 17.4 - - - +
71A ALA 5.0 2.6 + - - -
72A VAL* 3.7 32.3 - - + +
186A PHE* 3.6 20.6 - - + -
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Residues in contact with LEU 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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22A LEU* 3.9 25.1 - - + -
27A ILE* 5.8 1.6 - - + -
30A LEU* 3.8 29.4 - - + -
31A ILE* 5.9 0.2 - - + -
56A PHE* 2.8 30.8 + - + +
57A VAL 4.0 2.5 - - - +
59A ARG* 1.3 78.5 - - - +
61A VAL* 1.3 59.9 + - + +
63A THR* 3.1 4.4 + - + -
64A LEU* 2.9 60.3 + - + +
163A PHE* 4.8 1.3 - - + -
186A PHE* 3.8 41.8 - - + -
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Residues in contact with VAL 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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31A ILE* 3.2 37.9 - - + -
39A VAL* 4.6 4.7 - - + -
43A ILE* 3.9 11.9 - - + -
57A VAL* 2.9 24.4 + - + +
58A ALA 4.0 2.5 - - - +
60A LEU* 1.3 74.3 - - + +
62A HIS* 1.3 57.3 + - - +
64A LEU* 3.2 12.4 + - + +
65A LYS* 2.9 31.4 + - + +
171A PHE* 4.4 17.4 - - + -
173A LEU* 3.8 29.6 - - + -
178A ILE* 4.7 3.6 - - + -
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Residues in contact with HIS 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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43A ILE* 3.6 29.0 - - + +
46A TYR* 3.9 32.6 + + + -
58A ALA 3.0 17.2 + - - +
59A ARG* 3.7 12.8 - - - +
61A VAL* 1.3 78.7 - - - +
63A THR* 1.3 66.8 + - - +
65A LYS* 3.4 8.8 + - - +
66A LEU* 3.1 56.1 + - + +
68A LYS* 5.0 7.3 - - + +
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Residues in contact with THR 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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59A ARG* 3.0 14.1 + - - -
60A LEU 3.3 9.0 - - - +
62A HIS* 1.3 82.2 - - - +
64A LEU* 1.3 54.3 + - + +
66A LEU 3.4 0.5 + - - -
67A GLY* 2.7 31.5 + - - -
68A LYS* 3.0 36.7 + - - +
69A PRO* 4.9 0.7 - - + -
70A ALA* 3.4 20.4 - - - +
165A PHE* 3.6 28.4 - - + -
186A PHE* 3.5 20.2 - - + -
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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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22A LEU* 4.3 3.1 - - + -
27A ILE* 4.0 33.4 - - + -
60A LEU* 2.9 48.0 + - + +
61A VAL* 3.2 9.2 + - + +
63A THR* 1.3 70.3 - - - +
65A LYS* 1.3 65.3 + - - +
67A GLY* 3.4 8.3 + - - +
165A PHE* 3.6 43.5 - - + -
171A PHE* 4.0 21.8 - - + -
178A ILE* 4.8 0.9 - - - -
180A ILE* 3.7 21.2 - - + +
181A PRO* 3.4 13.2 - - - +
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Residues in contact with LYS 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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43A ILE* 6.2 2.7 - - - -
61A VAL* 2.9 18.2 + - - +
62A HIS* 3.9 9.2 - - - +
64A LEU* 1.3 76.4 - - - +
66A LEU* 1.3 72.2 + - + +
173A LEU* 5.4 5.8 - - - -
176A GLU* 2.7 32.8 + - - -
178A ILE* 3.8 38.5 - - + +
179A GLU 4.9 1.6 - - - +
181A PRO* 3.6 13.0 - - - +
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Residues in contact with LEU 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 HIS* 3.1 49.4 + - + +
63A THR 4.1 0.2 - - - +
65A LYS* 1.3 90.1 - - + +
67A GLY* 1.3 62.7 + - - +
68A LYS* 3.3 29.6 + - + +
181A PRO* 3.5 11.8 - - - +
182A ASN* 4.2 3.1 - - - +
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Residues in contact with GLY 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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63A THR 2.7 13.2 + - - -
64A LEU 3.4 6.2 + - - -
66A LEU* 1.3 76.1 - - - +
68A LYS* 1.3 58.9 + - - +
69A PRO* 3.6 6.1 - - - +
165A PHE* 4.3 11.9 - - - -
181A PRO* 3.6 17.5 - - - +
182A ASN* 2.7 39.4 + - - -
183A SER 4.4 0.2 - - - +
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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