Contacts of the helix formed by residues 52 - 65 (chain A) in PDB entry 3EOV
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.4 8.3 + - + +
49A GLY 3.8 2.7 - - - -
51A ASP* 1.3 81.2 - - + +
53A PRO* 1.3 56.8 - - - +
55A THR* 4.1 9.2 - - - -
56A THR* 2.8 32.4 + - - +
109A GLU* 2.9 24.7 - - + +
110A ASN* 4.8 1.6 - - + -
149A VAL* 4.4 16.2 - - + -
150A VAL 4.9 3.8 - - - +
151A PHE* 4.4 10.8 - - + -
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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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49A GLY 3.3 19.3 - - - +
50A LYS 4.0 6.7 - - - +
51A ASP 3.7 3.8 - - - +
52A ALA* 1.3 89.3 - - - +
54A LEU* 1.3 69.9 + - + +
56A THR* 3.3 3.4 + - - +
57A GLU* 3.0 33.5 + - + +
109A GLU* 3.4 9.4 - - - +
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Residues in contact with LEU 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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53A PRO* 1.3 76.9 - - + +
55A THR* 1.3 54.9 + - - +
57A GLU* 4.5 0.4 - - - -
58A ASN* 3.0 15.9 + - - +
102A TYR* 2.4 49.2 + - + +
106A PHE* 5.1 6.1 - - + -
109A GLU* 2.5 38.2 + - + +
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Residues in contact with THR 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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52A ALA* 4.0 7.2 - - - -
54A LEU* 1.3 78.4 - - - +
56A THR* 1.3 61.3 + - - +
58A ASN* 3.4 4.0 + - - +
59A PHE* 3.1 20.6 + - - +
106A PHE* 3.5 23.6 - - + -
109A GLU* 2.9 28.1 + - - +
122A MET* 3.9 21.8 - - + +
130A ASN* 5.0 0.9 + - - -
149A VAL* 4.2 11.7 - - + +
151A PHE* 3.7 33.0 - - + -
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Residues in contact with THR 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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47A LEU* 4.0 17.8 - - + +
48A PHE 3.4 26.7 - - - +
49A GLY* 3.7 11.8 - - - +
52A ALA 2.8 25.3 + - - +
53A PRO* 3.3 6.8 + - - +
55A THR* 1.3 72.9 - - - +
57A GLU* 1.3 67.5 + - - +
59A PHE* 3.7 7.2 - - - +
60A ARG* 2.9 30.5 + - - +
151A PHE* 3.9 26.2 - - + +
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Residues in contact with GLU 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 PRO* 3.0 23.2 + - + +
54A LEU 3.5 4.5 - - - +
56A THR* 1.3 83.5 + - - +
58A ASN* 1.3 65.9 + - - +
60A ARG* 2.4 40.6 + - - +
61A GLN* 3.0 45.9 + - - +
101A ILE* 4.1 2.2 - - - -
102A TYR* 3.6 9.0 - - - +
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Residues in contact with ASN 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 LEU 3.0 12.4 + - - +
55A THR 3.4 9.6 - - - +
57A GLU* 1.3 78.9 - - - +
59A PHE* 1.3 64.7 + - - +
61A GLN* 3.9 1.7 - - - +
62A LEU* 3.2 34.1 + - - +
71A TYR* 5.4 0.2 + - - -
100A SER* 3.5 10.5 - - - +
101A ILE* 3.0 43.3 - - - +
102A TYR* 3.7 9.8 + - + -
106A PHE* 3.2 15.8 - - + -
122A MET* 4.7 4.0 - - - +
131A GLY 3.0 23.0 - - - +
132A SER* 4.9 0.2 - - - -
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Residues in contact with PHE 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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29A VAL* 3.9 17.3 - - + -
31A PHE* 3.9 24.2 - + - -
45A ILE* 4.5 4.9 - - + -
47A LEU* 3.9 14.4 - - + -
55A THR 3.1 7.3 + - - +
56A THR* 3.7 8.1 - - - +
58A ASN* 1.3 80.2 - - - +
60A ARG* 1.3 64.3 + - - +
62A LEU* 3.0 15.5 + - - +
63A CYS* 3.1 31.7 + - - -
71A TYR* 3.7 25.7 - + - -
120A LEU* 3.9 15.9 - - + -
122A MET* 5.3 3.6 - - - -
134A PHE* 3.8 24.0 - + + -
151A PHE* 3.4 36.3 - + + -
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Residues in contact with ARG 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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27A ALA* 4.7 14.6 - - + -
29A VAL* 4.2 23.1 - - + +
47A LEU* 4.3 6.7 - - + +
56A THR 2.9 21.4 + - - +
57A GLU* 2.4 54.2 + - - +
59A PHE* 1.3 73.6 - - - +
61A GLN* 1.3 69.1 + - - +
63A CYS* 3.0 18.4 + - - +
64A THR* 3.1 18.1 + - + +
66A GLU* 3.5 22.4 + - - -
186A GLU* 2.8 32.3 + - - +
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Residues in contact with GLN 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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57A GLU* 3.0 43.1 + - - +
58A ASN 4.0 2.7 - - - +
60A ARG* 1.3 84.9 - - - +
62A LEU* 1.3 58.3 + - - +
64A THR* 3.3 2.5 + - - -
65A GLY* 3.1 21.3 + - - -
66A GLU* 3.1 36.6 + - - +
67A HIS* 2.4 47.6 + - + +
69A PHE 4.6 0.9 - - - +
101A ILE* 3.4 19.3 - - + +
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Residues in contact with LEU 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 ASN* 3.2 35.0 + - - +
59A PHE* 3.0 3.0 + - - +
61A GLN* 1.3 78.2 - - - +
63A CYS* 1.3 64.8 + - - +
65A GLY* 3.8 2.8 + - - -
67A HIS* 5.7 0.4 - - + -
69A PHE* 3.6 38.8 - - + +
70A GLY* 3.1 12.2 - - - -
71A TYR* 3.0 65.0 + - + +
72A LYS 4.7 0.3 + - - -
90A PHE* 4.1 9.0 - - + -
99A LYS 4.3 2.5 - - - +
101A ILE* 4.0 8.5 - - + -
132A SER* 3.9 16.6 - - - -
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Residues in contact with CYS 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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29A VAL* 3.8 19.3 - - + -
31A PHE* 3.8 28.3 - - - -
59A PHE* 3.1 33.6 + - - -
60A ARG 3.0 11.3 + - - +
62A LEU* 1.3 79.6 - - - +
64A THR* 1.3 60.8 + - + +
71A TYR* 4.0 4.5 - - - -
72A LYS* 5.6 1.2 - - - +
184A SER* 2.7 36.9 + - - +
185A GLY* 3.6 17.5 - - - +
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Residues in contact with THR 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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60A ARG* 3.1 12.7 + - - +
61A GLN* 3.3 5.0 + - - -
63A CYS* 1.3 80.3 - - - +
65A GLY* 1.3 60.4 + - - +
66A GLU* 2.9 39.7 + - - +
184A SER 4.9 1.6 - - - +
185A GLY* 4.8 5.6 - - - -
186A GLU* 3.7 37.2 - - + +
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Residues in contact with GLY 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 GLN 3.1 7.6 + - - -
62A LEU 3.8 3.3 + - - -
63A CYS 3.5 1.4 - - - -
64A THR* 1.3 81.1 + - - +
66A GLU* 1.3 54.9 + - - +
67A HIS 3.2 2.9 - - - -
68A GLY* 2.7 33.3 + - - -
69A PHE 3.4 20.0 - - - -
70A GLY* 4.8 1.3 - - - -
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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