Contacts of the strand formed by residues 75 - 86 (chain B) in PDB entry 4DI2
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 LYS 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A VAL* 3.3 33.2 + - + +
1A GLU 4.0 6.7 + - - -
3A VAL* 3.3 30.3 + - + +
4A ASP* 5.1 7.9 - - - +
89A HIS* 5.6 2.6 + - - -
68B TYR* 5.2 5.2 - - + -
69B VAL 3.3 14.1 - - - +
70B PRO* 3.9 11.4 - - + -
71B TYR* 4.6 1.6 - - - -
73B GLN 6.0 1.1 - - - -
74B GLY* 1.3 76.6 - - - +
76B TRP* 1.3 63.5 + - - +
105B SER* 3.4 3.3 - - - -
106B ASP* 2.8 65.2 + - + +
108B PHE* 3.7 6.0 - - - +
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Residues in contact with TRP 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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0A VAL* 4.2 4.9 - - - -
37B ASN* 4.2 11.9 - - + -
39B ALA* 3.3 20.2 - - + +
67B VAL* 3.7 28.7 - - + -
68B TYR* 3.3 5.2 - - - +
69B VAL* 3.0 60.9 + - + +
71B TYR* 3.0 35.9 + + - -
75B LYS* 1.3 74.7 - - - +
77B GLU* 1.3 71.6 + - - +
78B GLY* 4.2 2.0 - - - -
100B ALA* 3.5 25.6 - - + -
102B ILE* 3.8 24.6 - - + +
104B GLU 3.4 13.2 - - - +
105B SER* 3.9 6.1 - - - +
108B PHE* 3.7 28.3 - + + -
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Residues in contact with GLU 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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-1A PHE* 4.8 2.3 - - - +
0A VAL* 3.8 15.0 - - + +
3A VAL* 4.0 4.3 - - - +
180A ASP* 2.7 39.8 - - - +
182A SER* 3.3 8.0 + - - +
67B VAL 3.2 13.0 - - - +
68B TYR* 3.6 8.6 - - + +
76B TRP* 1.3 80.0 - - - +
78B GLY* 1.3 59.3 + - - +
102B ILE* 3.7 2.9 - - - -
103B THR* 3.1 17.4 + - - +
104B GLU* 2.9 57.5 + - + +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A SER* 5.4 0.9 - - - -
66B GLY* 3.6 4.9 - - - -
67B VAL* 2.9 36.0 + - - +
76B TRP* 4.0 3.6 - - - -
77B GLU* 1.3 76.8 - - - +
79B GLU* 1.3 66.8 + - - +
101B ALA 2.9 16.6 - - - -
102B ILE* 4.2 0.2 - - - -
103B THR* 3.6 8.7 - - - -
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 2.7 39.2 + - - +
60B TYR* 5.7 0.9 - - - +
62B ASP* 5.3 5.2 - - - +
65B LYS 3.8 6.7 - - - +
66B GLY* 5.4 2.7 - - - -
78B GLY* 1.3 79.2 - - - +
80B LEU* 1.3 66.8 + - - +
99B ILE 3.7 0.9 - - - +
100B ALA* 4.5 1.1 - - - -
101B ALA* 2.8 40.0 + - - +
103B THR* 3.9 19.3 + - + +
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Residues in contact with LEU 80 (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 TYR* 4.7 1.8 + - - -
62B ASP* 3.2 10.7 - - - +
63B LEU* 3.0 35.4 + - + +
64B ARG 3.8 1.9 + - - -
65B LYS* 2.9 41.3 + - + +
66B GLY 4.1 7.0 - - - +
67B VAL* 3.8 22.9 - - + -
79B GLU* 1.3 73.2 - - - +
81B GLY* 1.3 57.0 + - - +
98B ASN* 5.5 0.2 - - + -
99B ILE 3.7 6.1 - - - +
100B ALA* 4.1 15.0 - - + +
129B PRO* 3.9 25.1 - - + -
133B LEU* 3.8 35.9 - - + -
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Residues in contact with GLY 81 (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 TYR* 4.4 9.4 - - - -
61B ARG 3.1 13.9 - - - -
62B ASP* 4.3 1.3 - - - -
63B LEU* 3.7 11.8 - - - +
79B GLU 3.8 0.2 + - - -
80B LEU* 1.3 76.1 - - - +
82B THR* 1.3 60.0 + - - +
98B ASN* 3.5 5.4 - - - +
99B ILE* 2.8 38.3 + - - -
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Residues in contact with THR 82 (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 TYR* 3.5 4.7 - - - -
61B ARG* 2.8 48.5 + - - +
63B LEU* 4.2 13.8 - - + +
81B GLY* 1.3 75.1 - - - +
83B ASP* 1.3 64.1 + - - +
96B ARG* 3.2 29.7 + - + -
97B ALA 3.3 13.5 - - - +
98B ASN* 3.5 25.1 - - - +
99B ILE* 4.5 1.8 - - - +
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Residues in contact with ASP 83 (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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21B GLY* 3.4 11.9 - - - +
52B TYR* 2.6 28.8 + - - +
57B SER* 2.7 24.0 + - - -
59B THR* 2.7 31.2 + - - -
60B TYR* 3.4 11.4 - - - +
82B THR* 1.3 74.6 - - - +
84B LEU* 1.3 74.4 + - - +
85B VAL* 3.6 4.6 - - - +
95B VAL 3.6 0.2 - - - +
96B ARG* 3.4 13.1 - - - +
97B ALA 3.0 29.2 + - - +
99B ILE* 3.6 12.9 - - + +
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Residues in contact with LEU 84 (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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19B THR 3.8 0.3 - - - +
20B VAL* 3.4 3.5 - - - -
21B GLY 2.8 32.8 + - - +
22B SER* 3.8 19.5 - - - +
59B THR* 3.9 22.4 - - + +
83B ASP* 1.3 82.5 + - - +
85B VAL* 1.3 59.6 + - - +
94B THR* 3.8 21.1 - - + +
95B VAL* 3.3 5.8 - - - +
96B ARG* 3.9 37.0 - - + +
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Residues in contact with VAL 85 (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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18B MET* 3.5 31.9 - - + -
19B THR 3.3 9.9 - - - +
20B VAL* 4.0 8.3 - - + -
38B PHE* 3.9 25.4 - - + -
83B ASP 3.6 11.4 - - - +
84B LEU* 1.3 80.7 - - - +
86B SER* 1.3 69.8 + - - +
93B VAL 4.1 0.7 - - - +
94B THR* 3.5 2.3 - - - +
95B VAL* 2.8 36.5 + - - +
97B ALA* 4.0 12.8 - - + -
99B ILE* 4.0 5.8 - - + -
136B PHE* 3.7 16.6 - - + -
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Residues in contact with SER 86 (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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18B MET* 3.2 8.8 - - - +
19B THR* 2.8 48.1 + - - -
85B VAL* 1.3 73.8 + - - +
87B ILE* 1.3 68.1 + - - +
88B PRO* 3.9 2.2 - - - -
93B VAL 3.4 10.1 + - - -
94B THR* 2.8 30.1 + - - +
136B PHE* 6.1 0.4 - - - -
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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