Contacts of the helix formed by residues 60 - 69 (chain B) in PDB entry 4DF3
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 SER 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 5.3 0.7 - - - -
55B TRP* 2.9 33.8 + - - -
56B ASN 3.1 9.5 + - - -
57B ALA 3.6 7.9 + - - +
59B ARG* 1.3 78.6 - - - +
61B LYS* 1.4 64.2 + - - +
62B LEU 3.7 3.6 + - - -
63B ALA* 3.2 2.3 + - - +
64B ALA 3.1 17.2 + - - -
90B THR* 4.3 9.6 - - - -
91B THR* 2.7 31.2 + - - +
301B SAM 4.8 0.4 - - - -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG 4.2 0.6 + - - +
60B SER* 1.4 73.1 + - - +
62B LEU* 1.3 57.8 + - - +
64B ALA* 3.3 6.7 + - - +
65B ALA* 2.9 27.7 + - - +
91B THR* 4.2 3.0 + - - -
152B TYR* 4.0 4.9 + - - +
154B ASP* 2.8 32.5 + - - +
181B ALA* 3.5 24.5 - - + -
217B LEU* 3.6 22.7 - - + +
221B ASP* 3.6 19.3 + - + +
224B HIS* 3.5 37.9 - - + -
226B MET* 3.8 10.1 - - + -
301B SAM 4.0 21.5 + - - +
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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
----------------------------------------------------------
55B TRP* 3.9 29.2 - - + -
60B SER* 3.3 1.4 + - - -
61B LYS* 1.3 75.6 - - - +
63B ALA* 1.3 65.2 + - - +
65B ALA* 3.2 2.7 + - + +
66B LEU* 3.1 23.0 + - + +
70B LEU* 4.4 17.9 - - + -
73B LEU* 4.6 11.9 - - + -
75B VAL* 4.2 17.3 - - + -
91B THR* 4.0 6.5 - - + -
95B MET* 3.9 30.1 - - + -
98B ILE* 6.2 0.2 - - + -
152B TYR* 3.5 20.7 + - + +
179B LEU* 4.3 19.1 - - + -
226B MET* 4.0 8.7 - - + -
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Residues in contact with ALA 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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28B ILE* 4.0 10.3 - - + -
55B TRP* 3.5 48.0 - - + +
57B ALA* 3.9 17.0 - - - -
60B SER* 3.2 10.9 + - - +
62B LEU* 1.3 75.5 - - - +
64B ALA* 1.3 64.1 + - - +
65B ALA 3.3 0.2 + - - -
66B LEU* 3.3 7.8 + - - +
67B LEU* 3.1 25.3 + - - +
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Residues in contact with ALA 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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57B ALA* 3.6 15.8 - - - +
60B SER 3.1 7.8 + - - +
61B LYS* 3.5 12.3 - - - +
62B LEU 3.3 0.2 - - - -
63B ALA* 1.3 77.7 - - - +
65B ALA* 1.3 62.0 + - - +
67B LEU* 3.3 2.2 + - - +
68B LYS* 2.9 26.3 + - - +
217B LEU* 3.9 17.9 - - + -
220B PHE* 3.4 32.5 - - + -
221B ASP* 4.7 1.8 - - + +
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Residues in contact with ALA 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 LYS 2.9 13.6 + - - +
62B LEU* 3.2 10.7 + - - +
64B ALA* 1.3 75.8 - - - +
66B LEU* 1.3 53.4 + - - +
68B LYS* 3.3 1.8 + - - -
69B GLY 3.0 9.4 + - - -
70B LEU* 2.8 41.1 + - + -
215B VAL* 3.9 8.4 - - + +
217B LEU* 3.4 19.0 - - + +
226B MET* 3.8 25.1 - - + -
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Residues in contact with LEU 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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13B TRP* 3.3 60.6 - - + +
16B VAL* 4.5 1.8 - - + -
28B ILE* 4.7 3.8 - - + -
55B TRP* 3.9 30.3 - - + -
62B LEU* 3.1 15.8 + - + +
63B ALA* 3.6 8.1 - - - +
65B ALA* 1.3 75.1 - - - +
67B LEU* 1.3 65.2 + - - +
69B GLY* 3.1 13.5 + - - -
70B LEU* 4.2 14.3 + - + +
72B GLU 4.2 7.9 - - - +
73B LEU* 3.9 39.9 - - + -
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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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13B TRP* 4.3 12.6 - - + -
28B ILE* 3.8 37.5 - - + +
57B ALA* 3.4 26.9 - - + -
63B ALA 3.1 14.2 + - - +
64B ALA 3.8 3.6 - - - +
66B LEU* 1.3 76.4 - - - +
68B LYS* 1.3 62.8 + - - +
69B GLY* 3.5 0.5 + - - -
220B PHE* 3.7 28.0 - - + -
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Residues in contact with LYS 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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64B ALA 2.9 21.0 + - - +
65B ALA* 4.0 0.4 - - - +
66B LEU 3.1 0.2 - - - -
67B LEU* 1.3 79.8 - - - +
69B GLY* 1.3 55.6 + - - +
215B VAL* 3.3 28.4 - - + +
216B HIS* 2.9 30.3 + - - +
217B LEU* 4.2 4.9 - - - +
218B ASP* 2.8 30.4 + - - +
219B PRO* 4.7 1.8 - - + -
220B PHE* 3.7 26.7 - - + -
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Residues in contact with GLY 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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65B ALA 3.0 1.0 + - - -
66B LEU 3.1 8.6 + - - -
67B LEU 3.4 1.3 - - - -
68B LYS* 1.3 80.1 - - - +
70B LEU* 1.3 73.1 + - - +
71B ILE* 3.1 9.0 + - - +
213B ASP* 3.7 4.1 - - - +
215B VAL* 4.6 4.0 - - - -
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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