Contacts of the helix formed by residues 64 - 72 (chain B) in PDB entry 3DC1
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 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B LYS 4.3 0.9 - - - -
50B THR* 4.7 1.8 - - - -
62B GLN* 3.8 6.8 + - - +
63B PHE* 1.3 75.3 - - - +
65B GLU* 1.3 74.6 + - - -
66B GLU* 3.3 2.2 - - - -
67B MET* 3.0 10.3 + - - +
68B MET* 2.9 20.3 + - - +
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Residues in contact with GLU 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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49B LYS* 3.4 22.3 + - + +
50B THR* 3.9 15.8 - - + +
64B GLY* 1.3 77.5 - - - +
66B GLU* 1.3 63.9 + - - +
68B MET* 3.3 2.6 + - - +
69B LYS* 3.2 28.9 + - + +
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Residues in contact with GLU 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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64B GLY 3.3 0.6 - - - -
65B GLU* 1.3 81.4 - - - +
67B MET* 1.3 59.1 + - - +
69B LYS* 3.4 38.7 + - - +
70B ARG* 3.4 17.3 + - - +
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Residues in contact with MET 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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62B GLN 4.5 2.2 - - - +
63B PHE* 3.8 26.0 - - + -
64B GLY* 3.0 16.3 + - - +
66B GLU* 1.3 75.4 - - - +
68B MET* 1.3 59.8 - - - +
70B ARG* 3.1 22.6 + - - +
71B ALA* 2.8 25.1 + - - +
82B GLU* 6.0 0.2 - - - +
301B LEU* 3.9 37.5 - - + -
305B GLN* 4.2 16.8 - - + +
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Residues in contact with MET 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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53A ILE* 4.3 3.4 - - + -
48B PHE* 3.5 28.7 - - + +
49B LYS* 3.3 24.2 - - - +
50B THR* 3.1 41.3 - - - +
51B ALA* 3.6 13.0 - - + +
63B PHE* 4.2 9.1 - - + +
64B GLY 2.9 10.5 + - - +
65B GLU 3.5 1.8 - - - +
67B MET* 1.3 75.4 - - - +
69B LYS* 1.3 67.1 + - + +
71B ALA* 2.9 13.8 + - - +
72B LEU* 2.9 28.4 + - + +
298B PHE* 3.6 27.1 - - + -
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Residues in contact with LYS 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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43B PRO* 4.0 35.7 - - + +
44B ASN* 2.8 33.7 + - - +
49B LYS* 6.2 4.3 - - + +
65B GLU* 3.2 21.1 + - + +
66B GLU* 3.4 37.7 + - - +
67B MET 3.4 0.2 - - - -
68B MET* 1.3 78.3 - - + +
70B ARG* 1.3 61.9 - - - +
72B LEU* 3.2 13.4 + - + +
73B GLN* 3.1 20.8 + - - +
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Residues in contact with ARG 70 (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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66B GLU 3.4 7.7 + - - +
67B MET* 3.1 26.1 + - - +
69B LYS* 1.3 78.9 - - - +
71B ALA* 1.4 62.2 + - - +
73B GLN* 3.3 18.9 + - - +
74B TYR 4.9 0.9 - - - +
75B SER* 5.9 1.4 - - - -
76B PRO* 5.9 1.2 - - - +
80B ILE* 3.8 21.0 - - - +
81B PRO* 4.0 8.5 - - - +
82B GLU* 2.9 43.6 + - - -
297B THR* 3.6 14.4 - - + +
301B LEU* 3.9 26.1 - - + +
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Residues in contact with ALA 71 (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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268A GLY* 4.0 5.9 - - - -
269A LEU* 4.4 0.2 - - - +
63B PHE* 4.2 8.1 - - + -
67B MET 2.8 12.8 + - - +
68B MET* 2.9 12.9 + - - +
70B ARG* 1.4 77.6 - - - +
72B LEU* 1.3 58.9 + - - +
73B GLN 3.3 1.8 - - - -
297B THR* 3.6 5.3 - - - -
298B PHE* 3.1 57.8 + - + +
301B LEU* 4.1 13.9 - - + -
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Residues in contact with LEU 72 (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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266A SER* 3.0 17.3 + - - +
267A SER* 2.9 14.7 + - - -
268A GLY 2.7 25.1 + - - -
269A LEU* 3.9 17.3 - - + -
43B PRO 5.4 0.9 - - - +
46B PHE* 3.4 39.9 - - + -
48B PHE* 3.3 52.3 - - + +
68B MET* 2.9 30.5 + - + +
69B LYS* 3.2 7.6 + - + +
70B ARG 3.2 0.4 - - - -
71B ALA* 1.3 77.5 - - - +
73B GLN* 1.4 53.6 + - - +
298B PHE* 4.5 3.8 - - + -
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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