Contacts of the helix formed by residues 69 - 79 (chain B) in PDB entry 5YL4
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 GLU 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLN* 6.0 2.9 + - - +
67B ASP* 3.3 31.4 + - - +
68B LEU* 1.3 81.1 - - - +
70B PRO* 1.3 74.5 - - + +
71B GLY* 4.3 9.2 - - - +
72B THR* 4.5 6.0 + - - +
73B MET* 4.7 1.0 + - - +
92B PHE* 4.7 2.2 - - - +
93B GLY 3.7 4.0 - - - -
94B GLN 4.2 3.6 - - - +
95B SER 5.3 0.5 - - - -
96B GLY* 3.9 21.1 + - - +
97B ALA 5.7 0.4 - - - -
501B GDP 5.6 1.6 + - - -
251C ASP* 5.2 7.9 - - - +
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Residues in contact with PRO 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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69B GLU* 1.3 88.1 - - + +
71B GLY* 1.3 66.3 + - - +
72B THR 3.4 0.2 - - - -
73B MET* 2.9 6.9 + - + +
74B ASP* 2.8 39.7 + - - +
92B PHE* 4.2 22.0 - - + -
93B GLY 3.9 6.3 - - - +
94B GLN* 3.4 35.9 - - - +
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Residues in contact with GLY 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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69B GLU* 3.5 9.1 - - - +
70B PRO* 1.3 81.9 - - - +
72B THR* 1.3 58.2 + - - +
74B ASP* 3.3 8.1 + - - +
75B SER* 2.9 24.3 + - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.5 52.6 + - - +
14B ASN* 4.1 13.9 - - + -
15B GLN* 4.2 20.9 - - - +
67B ASP* 3.9 15.1 + - - -
69B GLU* 4.5 8.2 + - - +
70B PRO 3.4 0.6 - - - -
71B GLY* 1.3 73.1 - - - +
73B MET* 1.3 58.5 + - - +
75B SER* 3.2 10.2 + - - -
76B VAL* 3.0 26.2 + - + +
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Residues in contact with MET 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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14B ASN* 4.1 18.8 - - - +
65B LEU* 3.3 31.9 - - + +
66B VAL 3.8 1.3 - - - -
67B ASP* 3.5 34.8 - - + -
69B GLU 4.7 1.4 + - - +
70B PRO* 2.9 11.5 + - + +
72B THR* 1.3 75.1 - - - +
74B ASP* 1.3 64.4 + - - +
76B VAL* 3.5 6.3 + - - +
77B ARG* 3.3 27.8 + - - +
90B PHE* 3.6 25.3 - - + -
91B VAL 3.5 9.0 - - - +
92B PHE* 3.4 35.9 - - + -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 2.8 34.9 + - - +
71B GLY* 3.5 10.8 + - - +
73B MET* 1.3 73.1 - - - +
75B SER* 1.3 56.2 + - - +
77B ARG* 3.4 24.2 + - - +
78B SER* 3.1 32.8 + - - +
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Residues in contact with SER 75 (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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15B GLN* 5.2 6.7 - - - -
71B GLY 2.9 16.7 + - - -
72B THR* 3.2 15.8 + - - -
74B ASP* 1.3 75.6 - - - +
76B VAL* 1.3 60.6 + - - +
78B SER* 3.8 5.5 - - - -
79B GLY* 2.9 25.1 + - - -
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Residues in contact with VAL 76 (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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8B GLN* 4.7 0.2 - - - +
14B ASN* 3.8 36.1 - - + +
15B GLN* 5.3 4.9 - - - +
18B ALA* 4.3 13.7 - - + -
65B LEU* 3.6 25.8 - - + -
72B THR* 3.0 19.4 + - + +
73B MET* 3.8 9.9 - - - +
74B ASP 3.3 0.4 - - - -
75B SER* 1.3 74.6 - - - +
77B ARG* 1.3 66.8 + - - +
79B GLY* 3.1 12.1 + - - -
82B GLY* 3.2 15.9 + - - -
85B PHE* 4.0 21.1 - - + -
90B PHE* 4.4 3.1 - - + -
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Residues in contact with ARG 77 (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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73B MET* 3.3 17.2 + - - +
74B ASP* 3.8 26.6 + - - +
75B SER 3.4 0.2 - - - -
76B VAL* 1.3 79.9 - - - +
78B SER* 1.3 59.2 + - - +
79B GLY 4.1 1.0 - - - +
82B GLY* 3.8 22.1 - - - +
83B GLN* 3.7 26.1 + - - +
87B PRO* 5.1 5.1 + - - +
90B PHE* 3.4 49.5 - - + +
92B PHE* 4.5 19.6 - - - -
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Residues in contact with SER 78 (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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74B ASP 3.1 17.5 + - - -
75B SER* 3.9 7.0 - - - -
77B ARG* 1.3 74.9 - - - +
79B GLY* 1.3 66.3 + - - +
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Residues in contact with GLY 79 (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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75B SER 2.9 16.9 + - - -
76B VAL* 3.1 7.3 + - - -
77B ARG 4.1 1.4 - - - +
78B SER* 1.3 83.4 - - - +
80B PRO* 1.3 76.1 - - - +
81B PHE 3.4 2.2 - - - -
82B GLY* 3.1 13.7 + - - -
83B GLN* 5.0 2.1 + - - +
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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