Contacts of the helix formed by residues 62 - 74 (chain B) in PDB entry 4B94
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 PRO 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B GLY* 1.4 80.5 - - - +
63B GLU* 1.3 68.5 + - - +
66B LEU* 2.8 32.6 + - - +
98B LEU* 3.7 8.7 - - + -
103B TYR* 3.5 46.7 - - + -
106B ASN* 3.7 15.9 - - - +
108B SER* 3.9 2.5 - - - -
109B PHE* 3.6 30.7 - - + +
112B ILE* 3.5 12.2 - - + +
1201B GOL 3.8 2.7 - - - +
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Residues in contact with GLU 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 PRO* 1.3 72.1 - - - +
64B ASP* 1.4 59.0 + - - +
66B LEU* 3.5 2.5 + - - +
67B SER* 3.0 29.7 + - - -
106B ASN* 2.9 28.2 + - - +
108B SER* 3.6 21.9 + - - +
1201B GOL 2.5 34.5 + - - +
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Residues in contact with ASP 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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-1B PRO* 3.8 17.0 - - + +
0B GLY 3.4 8.2 + - - +
62B PRO 3.4 0.4 - - - -
63B GLU* 1.4 76.1 - - - +
65B TRP* 1.3 63.4 + - - +
67B SER* 3.5 7.8 + - - -
68B LEU* 3.2 21.8 + - - +
1197B PGE 3.4 39.7 + - - +
1201B GOL 5.3 3.4 + - - -
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Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1B PRO* 3.6 27.8 + - + +
0B GLY 3.1 25.2 + - - +
62B PRO 3.8 3.6 - - - +
63B GLU 3.4 0.2 - - - -
64B ASP* 1.3 76.4 - - - +
66B LEU* 1.3 56.0 + - - +
68B LEU* 3.2 16.1 + - + +
69B LEU* 2.9 36.5 + - + +
90B ARG* 3.7 40.6 - - - -
93B GLN* 4.1 4.9 - - + -
94B ALA* 3.5 36.3 - - + -
97B ALA* 3.9 28.8 - - + +
98B LEU* 3.9 13.9 - - + +
112B ILE* 3.8 13.9 - - + -
1197B PGE 3.8 33.0 - - - -
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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
----------------------------------------------------------
62B PRO 2.8 22.2 + - - +
63B GLU* 3.9 3.4 - - - +
65B TRP* 1.3 71.1 - - - +
67B SER* 1.3 54.7 + - - +
69B LEU* 3.2 3.1 + - + -
70B LEU* 2.8 63.2 + - + +
91B TYR* 4.7 9.6 - - - +
108B SER* 3.9 22.9 - - - +
111B ARG* 3.9 49.6 - - + +
112B ILE* 3.9 24.6 - - + +
115B ARG* 6.1 0.4 - - + -
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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
----------------------------------------------------------
63B GLU 3.0 17.8 + - - -
64B ASP* 3.6 9.4 - - - -
65B TRP 3.3 0.2 - - - -
66B LEU* 1.3 75.7 - - - +
68B LEU* 1.4 60.4 + - - +
70B LEU* 4.1 6.7 - - - +
71B LYS* 3.2 24.3 + - - +
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Residues in contact with LEU 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 ASP 3.2 9.4 + - - +
65B TRP* 3.2 15.8 + - + +
67B SER* 1.4 77.1 - - - +
69B LEU* 1.3 66.8 + - + +
71B LYS* 3.4 10.2 + - - +
72B LEU* 3.0 29.8 + - + +
90B ARG* 3.8 46.9 - - + +
1197B PGE 3.8 32.8 - - - +
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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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65B TRP* 2.9 26.9 + - + +
66B LEU* 3.2 4.9 + - + +
68B LEU* 1.3 78.0 - - + +
70B LEU* 1.3 58.5 + - - +
72B LEU* 3.3 5.7 + - + +
73B GLU* 3.0 26.9 + - - +
87B LEU* 4.0 6.7 - - + +
90B ARG* 3.7 47.1 - - + +
91B TYR* 3.7 48.1 + - + +
94B ALA* 3.8 22.7 - - + -
112B ILE* 4.1 12.1 - - + -
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Residues in contact with LEU 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 47.0 + - + +
67B SER* 4.2 5.4 - - - +
69B LEU* 1.3 71.9 - - - +
71B LYS* 1.4 57.8 + - - +
73B GLU* 3.3 16.8 + - + +
74B LYS* 3.0 27.9 + - - +
91B TYR* 4.4 9.9 - - - +
111B ARG* 3.7 29.6 - - - +
115B ARG* 5.8 4.3 - - + -
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Residues in contact with LYS 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 3.2 19.7 + - - +
68B LEU* 3.6 9.0 - - - +
69B LEU 3.3 0.2 - - - -
70B LEU* 1.4 74.6 - - - +
72B LEU* 1.3 57.9 + - - +
74B LYS* 3.4 9.4 + - + +
75B ASN* 3.1 51.8 + - - +
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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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68B LEU* 3.0 16.3 + - + +
69B LEU* 3.3 10.3 + - + +
71B LYS* 1.3 72.2 - - - +
73B GLU* 1.4 56.0 + - - +
75B ASN* 3.2 12.0 + - + +
76B SER* 2.7 39.6 + - - +
86B LYS* 3.7 34.8 - - + +
87B LEU* 3.9 23.6 - - + +
90B ARG* 3.7 40.4 - - + +
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Residues in contact with GLU 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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69B LEU 3.0 10.5 + - - +
70B LEU* 3.3 19.7 + - + +
72B LEU* 1.4 75.1 - - - +
74B LYS* 1.4 60.9 + - - +
76B SER* 3.2 14.9 + - - -
77B VAL* 3.9 11.3 - - - +
79B LEU* 5.7 1.8 - - + +
87B LEU* 3.7 25.9 - - + +
91B TYR* 3.4 26.9 + - - -
115B ARG* 2.9 42.3 + - - +
119B LEU* 4.8 1.1 - - - +
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Residues in contact with LYS 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 LEU 3.0 13.3 + - - +
71B LYS* 3.6 13.0 - - + +
73B GLU* 1.4 75.2 - - - +
75B ASN* 1.3 65.3 + - - +
76B SER 3.4 2.8 + - - -
77B VAL* 3.9 18.2 + - - +
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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