Contacts of the helix formed by residues 52 - 65 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.4 6.6 + - + +
49B GLY 3.8 2.5 - - - -
51B ASP* 1.3 82.5 - - + +
53B PRO* 1.3 61.1 - - - +
55B THR* 3.9 12.1 - - + +
56B THR* 3.0 31.2 + - - +
109B GLU* 2.9 26.7 - - + +
110B ASN* 4.7 3.6 - - + +
149B VAL* 4.5 11.0 - - + -
150B VAL 4.9 4.3 - - - +
151B PHE* 4.8 8.1 - - + -
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Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLY 3.3 18.8 - - - +
50B LYS 4.6 4.5 - - - +
51B ASP 4.0 3.4 - - - +
52B ALA* 1.3 86.5 - - - +
54B LEU* 1.3 65.0 + - + +
56B THR* 3.0 5.0 + - - +
57B GLU* 2.8 40.1 + - + +
109B GLU* 2.9 17.5 - - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO* 1.3 76.8 - - + +
55B THR* 1.3 64.2 + - - +
57B GLU* 3.3 1.6 + - + -
58B ASN* 3.1 11.4 + - - +
102B TYR* 2.6 49.4 + - + +
106B PHE* 4.9 7.2 - - + -
109B GLU* 2.9 33.6 + - + +
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 3.8 7.9 - - - -
54B LEU* 1.3 77.9 - - - +
56B THR* 1.3 60.6 + - - +
58B ASN* 3.2 7.0 + - - +
59B PHE* 3.2 19.6 + - - +
106B PHE* 4.2 18.5 - - + -
109B GLU* 2.8 35.4 + - - +
122B MET* 4.1 20.3 - - + +
130B ASN* 5.9 0.5 + - - -
149B VAL* 3.9 11.8 - - + +
151B PHE* 3.7 36.6 - - + -
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.0 16.5 - - + +
48B PHE 3.6 34.1 - - - +
49B GLY* 3.8 8.8 - - - +
52B ALA 3.0 17.0 + - - +
53B PRO* 3.0 17.2 + - - +
55B THR* 1.3 74.3 - - - +
57B GLU* 1.3 61.2 + - - +
59B PHE* 3.3 7.6 + - - +
60B ARG* 2.8 32.0 + - - +
151B PHE* 3.9 19.1 - - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PRO* 2.8 27.0 + - + +
54B LEU* 4.8 1.3 - - + -
56B THR* 1.3 79.5 + - - +
58B ASN* 1.3 65.7 + - - +
60B ARG* 2.3 46.2 + - - +
61B GLN* 3.0 44.1 + - - +
101B ILE* 4.0 2.7 - - + -
102B TYR* 3.4 16.6 - - - +
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU 3.1 12.4 + - - +
55B THR 3.4 10.7 - - - +
57B GLU* 1.3 77.0 - - - +
59B PHE* 1.3 63.0 + - - +
61B GLN* 4.0 1.4 - - - +
62B LEU* 3.1 39.6 + - - +
71B TYR* 4.9 0.7 + - - -
100B SER* 3.3 11.8 - - - +
101B ILE* 3.0 47.1 - - - +
102B TYR* 4.1 8.1 - - + -
106B PHE* 3.8 10.5 - - + -
122B MET* 4.4 6.6 - - - +
131B GLY 3.0 21.1 - - - +
132B SER* 4.5 0.5 - - - -
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.6 28.0 - - + -
31B PHE* 3.7 26.5 - + - -
45B ILE* 4.3 12.1 - - + -
47B LEU* 3.9 18.6 - - + -
55B THR 3.2 7.1 + - - +
56B THR* 3.6 7.2 - - - +
57B GLU 3.3 0.2 - - - -
58B ASN* 1.3 82.7 + - - +
60B ARG* 1.3 62.4 + - - +
62B LEU* 3.3 3.0 + - - +
63B CYS* 3.2 33.9 + - - -
71B TYR* 3.5 31.6 - + - -
120B LEU* 4.5 4.0 - - + -
122B MET* 5.5 2.7 - - - -
134B PHE* 3.8 17.9 - + + -
151B PHE* 3.4 39.9 - + + -
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA* 4.5 13.7 - - + -
29B VAL* 4.4 18.5 - - + +
47B LEU* 4.5 7.6 - - + -
56B THR 2.8 21.2 + - - +
57B GLU* 2.3 44.7 + - - +
59B PHE* 1.3 72.9 - - - +
61B GLN* 1.3 78.5 + - - +
63B CYS* 3.2 14.2 + - - +
64B THR* 3.3 17.7 + - + +
66B GLU* 4.1 17.2 + - - -
186B GLU* 3.1 35.8 + - - +
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU* 3.0 40.4 + - - +
58B ASN 4.2 2.5 - - - +
60B ARG* 1.3 86.4 - - - +
62B LEU* 1.3 59.1 + - - +
64B THR* 3.0 14.7 + - - -
65B GLY* 3.1 10.4 + - - -
66B GLU* 3.4 35.4 + - - +
67B HIS* 2.5 45.6 + - + +
69B PHE 4.8 0.7 - - - +
101B ILE* 3.7 22.7 - - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASN* 3.1 38.3 + - - +
60B ARG 3.3 0.4 - - - -
61B GLN* 1.3 76.3 - - - +
63B CYS* 1.3 62.5 + - - +
65B GLY* 3.8 1.6 + - - -
67B HIS* 5.9 0.2 - - + -
69B PHE* 3.7 39.3 - - + +
70B GLY* 3.0 9.6 - - - -
71B TYR* 2.8 69.2 + - + +
72B LYS 4.6 0.2 + - - -
90B PHE* 4.0 11.0 - - + -
99B LYS 4.4 2.2 - - - +
101B ILE* 4.1 9.0 - - + -
132B SER* 3.8 19.1 - - - -
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Residues in contact with CYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.8 18.2 - - + -
30B TYR 4.8 0.4 - - - -
31B PHE* 4.0 13.7 - - - -
59B PHE* 3.2 41.8 + - - -
60B ARG 3.2 8.7 + - - +
62B LEU* 1.3 77.3 - - - +
64B THR* 1.3 64.7 + - - +
65B GLY* 4.5 0.2 - - - -
71B TYR* 3.9 12.6 - - - -
72B LYS* 5.2 2.3 + - - +
184B SER* 2.6 33.2 + - - +
185B GLY* 3.9 20.2 - - - +
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Residues in contact with THR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ARG* 3.5 13.2 - - + +
61B GLN 3.0 7.6 + - - -
63B CYS* 1.3 77.3 - - - +
65B GLY* 1.3 68.4 + - - +
66B GLU* 2.8 37.1 + - - +
72B LYS* 6.1 0.5 - - - +
184B SER 4.9 2.1 - - - +
185B GLY* 4.3 6.5 - - - -
186B GLU* 3.9 37.2 - - + +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN 3.1 8.4 + - - -
62B LEU 3.8 5.4 + - - -
63B CYS 3.4 1.8 - - - -
64B THR* 1.3 80.6 + - - +
66B GLU* 1.3 65.9 + - - +
67B HIS 3.3 2.0 - - - -
68B GLY* 2.8 20.4 + - - -
69B PHE 4.1 12.6 - - - -
70B GLY* 4.6 4.3 - - - -
72B LYS* 6.4 2.5 - - - -
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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