Contacts of the strand formed by residues 74 - 85 (chain B) in PDB entry 4BHT
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 ILE 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A MET* 6.2 3.8 - - + -
66B VAL* 3.4 31.9 - - + -
67B TRP 3.5 5.4 - - - +
68B VAL* 4.2 21.5 - - + +
72B ASN 3.9 4.2 + - - +
73B GLN* 1.3 77.4 - - - +
75B GLN* 1.3 66.2 + - - +
76B VAL* 4.4 5.9 + - + +
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Residues in contact with GLN 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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66B VAL* 3.4 5.8 - - - +
67B TRP* 2.8 74.3 + - + +
69B ASP* 2.8 29.0 + - + +
73B GLN* 3.9 16.9 - - - +
74B ILE* 1.3 76.8 + - - +
76B VAL* 1.3 64.2 + - - +
77B ASN* 4.6 2.7 - - - +
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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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64B ARG* 4.0 26.7 - - + -
65B VAL 3.6 3.1 - - - +
66B VAL* 4.5 15.5 - - + -
74B ILE* 5.1 5.4 - - + +
75B GLN* 1.3 81.5 + - - +
77B ASN* 1.3 73.3 + - - +
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Residues in contact with ASN 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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64B ARG* 3.7 5.0 - - - -
65B VAL* 2.8 36.5 + - - +
67B TRP* 2.9 30.0 + - - -
75B GLN* 4.6 2.4 - - - +
76B VAL* 1.3 83.2 + - - +
78B ARG* 1.3 61.6 + - - +
131B SER* 3.8 11.0 - - - +
132B ASP* 3.0 23.8 + - - +
133B PHE* 3.5 26.6 - - - +
134B ASP 5.0 0.4 - - - +
146B PHE* 4.2 8.1 - - + -
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Residues in contact with ARG 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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62B GLN* 3.4 44.7 + - + +
63B PHE 3.7 5.6 - - - +
64B ARG* 5.2 0.2 - - - +
65B VAL* 4.9 0.4 - - - -
77B ASN* 1.3 76.7 - - - +
79B ALA* 1.3 64.5 + - - +
80B TRP* 3.2 35.8 - - + -
131B SER* 2.8 27.6 + - - -
132B ASP* 3.1 22.8 + - - +
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Residues in contact with ALA 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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62B GLN* 3.4 3.6 - - - +
63B PHE* 3.0 60.9 + - + -
65B VAL* 3.8 7.2 - - + -
77B ASN 4.2 0.4 + - - -
78B ARG* 1.3 74.0 - - - +
80B TRP* 1.3 72.2 + - - +
95B MET* 6.0 0.2 - - + -
130B GLY 3.1 12.3 - - - +
131B SER* 4.0 2.7 - - - -
150B LEU* 3.8 18.6 - - + -
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Residues in contact with TRP 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 VAL* 4.2 6.5 - - + -
61B ILE 3.2 6.7 - - - +
62B GLN* 3.8 33.4 - - + +
63B PHE* 4.0 6.4 - - - -
78B ARG* 3.2 51.6 - - + -
79B ALA* 1.3 75.7 - - - +
81B ARG* 1.3 64.5 + - - +
82B VAL* 4.8 2.5 - - + +
95B MET* 4.0 7.3 - - - +
101B VAL* 3.7 34.5 - - + -
102B ASN* 3.8 5.4 - - + -
103B LEU* 3.9 42.7 - - + +
106B LEU* 3.5 29.2 - - + -
129B GLY* 3.1 1.8 - - - -
130B GLY 2.7 33.9 + - - +
132B ASP* 4.2 9.6 - - - -
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Residues in contact with ARG 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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59B ARG 4.0 0.2 - - - +
60B VAL* 3.5 2.1 - - - -
61B ILE* 3.0 40.9 + - + +
63B PHE* 4.2 0.6 - - - -
80B TRP* 1.3 72.8 - - - +
82B VAL* 1.3 63.6 + - - +
83B GLN* 3.6 13.6 + - + +
92B LYS 4.0 3.0 - - - -
93B GLY* 2.9 43.2 + - - +
94B GLY 3.1 17.4 + - - -
95B MET* 3.5 18.6 - - - -
127B GLY* 4.1 6.0 - - - -
128B LYS* 3.4 14.2 + - - +
129B GLY 3.3 8.5 - - - +
154B LEU* 3.9 25.4 - - + -
158B LEU* 4.6 1.8 - - + -
163B ASP* 2.7 45.7 + - - +
165B PRO* 3.8 13.9 - - - +
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Residues in contact with VAL 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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57B PRO* 4.3 5.8 - - + -
59B ARG 3.9 2.7 - - - -
60B VAL* 4.0 17.5 - - + -
80B TRP* 4.2 3.1 - - + -
81B ARG* 1.3 74.8 + - - +
83B GLN* 1.3 59.9 + - - +
84B PHE* 3.7 31.0 - - + +
103B LEU* 3.8 28.7 - - + -
106B LEU* 3.9 26.9 - - + +
107B LYS* 4.3 8.1 - - + +
110B GLY* 5.2 0.9 - - - -
127B GLY* 3.0 7.6 - - - -
128B LYS 2.5 38.5 + - - +
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Residues in contact with GLN 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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58B GLU 3.4 1.2 + - - -
59B ARG* 2.6 73.3 + - + +
61B ILE* 4.1 7.6 - - + +
81B ARG* 3.6 13.8 + - + +
82B VAL* 1.3 73.3 - - - +
84B PHE* 1.3 61.5 + - - +
91B TYR* 3.5 36.9 - - + -
126B GLY 4.2 0.2 - - - -
157B HIS* 3.1 30.5 + - - +
158B LEU* 4.4 0.2 - - - +
162B THR* 4.9 0.9 - - - +
163B ASP* 2.5 35.1 + - - +
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Residues in contact with PHE 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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24B PHE* 4.2 9.4 - + - -
54B LEU 3.3 25.8 - - - -
55B VAL 3.8 15.7 - - - -
56B GLU 4.7 0.9 - - - +
57B PRO* 3.8 28.8 - - + +
58B GLU* 3.1 26.9 + - - +
82B VAL* 3.4 21.8 + - + +
83B GLN* 1.3 73.1 - - - +
85B SER* 1.3 61.1 + - - +
91B TYR* 4.1 0.4 - - - -
107B LYS* 3.6 25.1 - - + -
110B GLY 3.9 7.4 - - - +
111B PHE* 3.6 37.5 - + + -
114B THR* 3.8 14.1 - - + +
126B GLY 2.8 17.6 + - - +
127B GLY* 4.7 0.2 - - - -
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Residues in contact with SER 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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54B LEU* 5.8 5.4 - - - +
58B GLU* 3.4 5.4 + - - -
84B PHE* 1.3 84.1 - - - +
86B SER* 1.3 62.3 + - - +
87B ALA* 3.2 22.2 + - - +
88B ILE* 4.9 0.9 + - - +
91B TYR* 3.4 9.1 - - - -
114B THR* 3.5 32.4 - - - +
125B GLY* 3.2 5.4 - - - -
126B GLY 2.8 29.0 + - - -
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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