Contacts of the helix formed by residues 58 - 69 (chain B) in PDB entry 3DBL
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 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ALA 3.8 2.6 + - - -
57B GLY* 1.3 75.0 - - - +
59B LEU* 1.3 62.6 + - - +
60B GLY 3.0 1.4 - - - +
61B CYS* 3.8 8.4 - - - +
62B GLU* 3.1 26.0 + - - +
90B ARG* 5.1 6.4 - - - +
91B GLN* 3.6 19.5 - - - +
92B PHE* 5.2 0.7 - - - -
296B ASN* 4.1 21.7 - - - +
176I GLY 4.2 0.2 - - - -
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Residues in contact with LEU 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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58B GLY* 1.3 73.3 - - - +
60B GLY* 1.3 57.9 + - - +
62B GLU* 3.6 1.4 - - - +
63B LEU* 2.9 40.1 + - + +
143B CYS 4.7 0.2 - - - +
144B GLY* 3.7 17.9 - - - -
180B GLY* 3.3 35.7 - - - +
181B GLY* 3.9 8.1 - - - +
182B THR* 4.8 1.3 - - - -
296B ASN* 3.6 18.5 + - - +
299B ILE* 3.8 14.8 - - + -
300B ALA* 3.7 32.5 - - + +
303B CYS* 5.9 0.2 - - - -
176I GLY* 3.3 37.2 + - - +
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Residues in contact with GLY 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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53B VAL* 4.5 3.7 - - - +
55B GLY 3.1 28.0 + - - -
56B ALA* 3.8 8.5 - - - -
57B GLY 4.0 2.2 - - - +
58B GLY 3.0 3.8 - - - +
59B LEU* 1.3 76.7 - - - +
61B CYS* 1.3 64.6 + - - -
63B LEU* 3.1 16.8 + - - +
64B LEU* 3.1 18.9 + - - +
144B GLY* 4.7 3.5 + - - -
176I GLY 4.6 0.8 + - - -
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Residues in contact with CYS 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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56B ALA* 3.7 22.7 - - - +
58B GLY* 3.7 9.4 + - - +
59B LEU 3.6 0.2 - - - -
60B GLY* 1.3 73.4 - - - +
62B GLU* 1.3 63.3 + - - +
64B LEU* 3.4 5.2 + - - +
65B LYS* 3.2 18.0 + - - +
91B GLN* 4.1 19.7 - - - -
92B PHE* 3.6 21.7 - - + -
93B LEU* 3.6 35.8 - - + +
94B PHE* 3.8 20.0 - - - -
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Residues in contact with GLU 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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44A GLU* 3.8 0.7 - - - +
47A LYS* 3.3 12.0 + - - -
48A ASN* 4.8 0.5 - - - +
495A ALA* 4.8 1.7 - - - +
58B GLY 3.1 18.2 + - - +
59B LEU* 4.3 0.2 - - - -
61B CYS* 1.3 79.1 - - - +
63B LEU* 1.3 51.2 + - - +
65B LYS* 2.4 34.0 + - - +
66B ASN* 2.8 45.8 + - - +
90B ARG 5.2 1.9 - - - +
92B PHE* 3.3 22.6 - - - -
293B ALA* 4.9 2.3 - - - +
296B ASN* 4.4 2.9 - - - +
297B ALA* 3.5 33.2 + - - +
300B ALA* 3.3 26.0 - - + -
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Residues in contact with LEU 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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53B VAL* 3.9 25.4 - - + -
59B LEU* 2.9 30.8 + - + +
60B GLY* 3.1 4.7 + - - +
62B GLU* 1.3 72.8 - - - +
64B LEU* 1.3 67.6 + - - +
66B ASN* 3.1 4.6 + - - +
67B LEU* 2.8 33.9 + - + +
142B VAL* 3.5 37.2 - - + -
143B CYS 4.4 15.7 - - - +
144B GLY* 4.5 1.3 - - - +
300B ALA* 3.6 25.6 - - + +
303B CYS* 4.1 9.0 - - + -
304B ALA* 4.3 11.2 - - + +
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Residues in contact with LEU 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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53B VAL* 4.0 10.3 - - + -
56B ALA* 5.3 0.7 - - + -
60B GLY 3.1 12.9 + - - +
61B CYS* 3.7 6.5 - - - +
63B LEU* 1.3 78.6 - - - +
65B LYS* 1.3 64.1 + - - +
67B LEU* 3.9 4.2 - - - +
68B ALA* 3.0 27.0 + - - +
75B ILE* 3.8 21.7 - - + +
77B VAL* 3.3 39.7 - - + -
93B LEU* 4.0 9.4 - - + -
107B ALA* 3.8 35.7 - - + +
111B LEU* 3.3 23.5 - - + +
120B VAL* 4.5 2.5 - - + -
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Residues in contact with LYS 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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44A GLU* 2.9 28.9 + - - +
47A LYS* 3.4 6.2 - - - +
74A PHE* 3.4 42.2 - - + -
75A PHE* 5.6 0.2 - - + -
491A HIS* 3.5 17.3 - - - +
495A ALA* 4.5 1.4 - - - +
61B CYS 3.2 11.0 + - - +
62B GLU* 2.4 39.4 + - - +
64B LEU* 1.3 82.9 - - - +
66B ASN* 1.3 87.3 + - - +
67B LEU 3.2 0.2 + - - -
68B ALA* 3.4 2.4 + - - +
69B LEU* 3.2 22.2 + - + +
92B PHE* 4.0 14.8 - - + -
111B LEU* 4.1 9.7 - - + +
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Residues in contact with ASN 66 (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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491A HIS* 3.5 11.3 - - - -
492A THR* 3.9 9.4 - - + +
495A ALA* 3.3 23.1 - - - +
62B GLU* 2.8 33.1 + - - +
63B LEU 3.1 3.1 + - - +
65B LYS* 1.3 85.7 - - - +
67B LEU* 1.3 60.9 + - - +
69B LEU* 3.6 3.6 + - - +
70B SER* 2.8 26.0 + - - -
300B ALA 3.5 8.9 + - - -
301B ALA* 3.5 29.7 - - - +
304B ALA* 3.6 17.9 - - + -
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Residues in contact with LEU 67 (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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51B VAL* 3.7 31.9 - - + -
53B VAL* 4.2 17.3 - - + -
63B LEU* 2.8 28.8 + - + +
64B LEU* 4.0 2.2 - - - +
66B ASN* 1.3 69.3 - - - +
68B ALA* 1.3 58.5 + - - +
69B LEU 3.0 1.3 - - - -
70B SER* 2.6 31.3 + - - -
71B GLY 3.4 5.4 + - - -
72B PHE* 3.5 23.1 + - + -
75B ILE* 4.3 13.5 - - + -
142B VAL* 4.6 7.0 - - + -
304B ALA* 3.8 25.4 - - + +
307B VAL* 4.1 23.6 - - + -
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Residues in contact with ALA 68 (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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17B TRP* 3.5 19.2 - - - -
64B LEU 3.0 18.4 + - - +
65B LYS 3.8 3.8 - - - +
67B LEU* 1.3 77.3 - - - +
69B LEU* 1.3 58.5 + - - +
70B SER 3.4 2.1 + - - -
71B GLY 3.8 1.7 + - - -
72B PHE 3.9 16.9 - - - +
75B ILE* 4.3 2.6 - - + +
111B LEU* 4.2 7.2 - - + -
115B VAL* 4.1 26.3 - - + +
118B CYS* 3.8 24.0 - - - -
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Residues in contact with LEU 69 (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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70A ALA 5.2 1.8 - - - +
71A GLY 3.4 24.4 - - - +
72A ASN* 3.7 12.8 - - - +
73A ASN 4.4 8.1 - - - +
74A PHE* 3.9 19.5 - - + +
491A HIS* 3.2 59.4 + - + +
17B TRP* 3.9 13.9 - - + -
20B VAL* 4.2 7.4 - - - +
65B LYS* 3.2 13.9 + - + +
66B ASN 3.8 0.9 - - - +
67B LEU 3.0 1.0 - - - -
68B ALA* 1.3 76.4 - - - +
70B SER* 1.3 60.1 + - - +
71B GLY 3.5 0.9 - - - -
115B VAL* 4.2 24.0 - - + -
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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