Contacts of the helix formed by residues 62 - 74 (chain B) in PDB entry 4DHI
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B GLU* 2.6 37.0 + - - +
61B THR* 1.3 76.5 - - - +
63B ALA* 1.3 63.6 + - - +
64B ALA* 3.6 6.7 + - - +
65B PHE* 3.0 20.1 + - - +
66B LEU* 3.1 20.1 + - - +
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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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62B SER* 1.3 71.5 - - - +
64B ALA* 1.3 54.9 + - - +
66B LEU* 3.6 14.5 - - + +
67B SER* 2.8 35.5 + - - -
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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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60B GLU* 4.5 5.2 - - - +
62B SER* 3.1 9.8 - - - +
63B ALA* 1.3 75.4 - - - +
65B PHE* 1.3 64.8 + - - +
67B SER* 3.5 4.6 + - - -
68B LYS* 3.1 23.9 + - - +
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Residues in contact with PHE 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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53B LEU* 4.4 5.8 - - + -
54B CYS* 4.1 21.5 - - - -
59B ASN* 3.3 48.5 - - + -
60B GLU* 3.6 32.5 + - + +
62B SER* 3.0 21.5 + - - +
64B ALA* 1.3 74.8 - - - +
66B LEU* 1.3 60.0 + - - +
68B LYS* 3.2 2.3 + - - -
69B ALA* 2.9 28.0 + - + +
234B MET* 3.6 49.9 - - + +
264B ARG* 4.3 8.7 - - + -
265B PRO* 6.2 2.5 - - + -
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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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54B CYS* 4.5 18.4 - - + -
62B SER 3.1 12.8 + - - +
63B ALA* 3.6 15.7 - - + +
65B PHE* 1.3 82.4 - - - +
67B SER* 1.3 53.2 + - - +
69B ALA* 3.7 2.4 - - - +
70B THR* 2.8 47.2 + - - +
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Residues in contact with SER 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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63B ALA 2.8 22.1 + - - -
64B ALA* 3.8 6.3 - - - -
66B LEU* 1.3 74.6 - - - +
68B LYS* 1.3 58.6 + - - +
70B THR* 3.3 7.7 + - - -
71B GLU* 2.9 37.6 + - - +
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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 3.1 17.0 + - - +
65B PHE* 3.7 3.8 - - - +
67B SER* 1.3 72.4 - - - +
69B ALA* 1.3 65.7 + - - +
71B GLU* 3.3 25.7 + - - +
72B LEU* 2.9 48.1 + - - +
232B GLU* 5.0 3.7 + - - -
233B TYR 3.6 9.2 - - - -
234B MET* 3.7 36.1 - - + +
244B TRP* 3.5 54.1 - - + +
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Residues in contact with ALA 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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50B PHE* 3.6 8.4 - - + -
53B LEU* 4.6 9.4 - - + -
54B CYS* 3.6 28.5 - - - -
65B PHE* 2.9 20.9 + - + +
66B LEU 3.7 2.0 - - - +
68B LYS* 1.3 76.6 - - - +
70B THR* 1.3 57.7 + - - +
72B LEU* 3.3 5.7 + - - +
73B SER* 2.9 30.9 + - - -
234B MET* 3.7 13.8 - - + +
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Residues in contact with THR 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 LEU* 2.8 37.2 + - - +
67B SER* 3.5 8.5 - - - -
68B LYS 3.2 0.2 - - - -
69B ALA* 1.3 76.5 - - - +
71B GLU* 1.3 63.8 + - + +
73B SER* 2.7 25.9 + - - +
74B GLU* 3.4 19.6 + - + +
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Residues in contact with GLU 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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67B SER* 2.9 24.7 + - - +
68B LYS* 3.3 32.7 + - + +
70B THR* 1.3 76.6 - - + +
72B LEU* 1.3 63.9 + - + +
74B GLU* 3.2 31.3 + - - +
75B VAL* 4.0 9.0 + - - +
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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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50B PHE* 3.6 22.9 - - + -
68B LYS* 2.9 41.1 + - - +
69B ALA* 3.3 0.6 + - - +
71B GLU* 1.3 78.0 - - + +
73B SER* 1.3 56.8 + - - +
74B GLU 3.1 0.2 - - - -
75B VAL* 3.0 7.3 + - + -
76B TYR* 2.8 56.1 + - + +
232B GLU* 3.9 22.4 - - + +
233B TYR 5.0 0.7 - - - +
234B MET* 3.6 30.5 - - - -
262B LEU* 3.9 17.3 - - + -
271B ILE* 5.5 0.4 - - + -
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Residues in contact with SER 73 (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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50B PHE* 3.7 17.2 - - - -
51B SER* 5.4 8.1 - - - -
69B ALA 2.9 15.2 + - - -
70B THR* 2.7 24.5 + - - +
72B LEU* 1.3 75.8 - - - +
74B GLU* 1.3 59.7 + - - +
75B VAL 3.2 0.2 - - - -
76B TYR 3.5 12.0 - - - +
274B LYS* 2.8 27.3 + - - -
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Residues in contact with GLU 74 (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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70B THR* 3.6 25.7 - - + +
71B GLU* 3.5 17.9 - - - +
72B LEU 3.1 0.8 - - - -
73B SER* 1.3 79.3 - - - +
75B VAL* 1.3 62.1 + - + +
274B LYS* 3.8 20.0 + - - +
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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