Contacts of the strand formed by residues 71 - 89 (chain B) in PDB entry 4R7X
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 TYR 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.9 7.6 + - - -
21A VAL* 3.6 38.8 - - + -
22A PRO* 3.3 26.3 - - + +
62B SER* 3.7 4.5 + - - -
63B ARG* 3.1 52.7 + - + +
64B ASN* 4.0 10.7 + - - -
70B ALA* 1.3 79.5 - - - +
72B THR* 1.3 75.2 + - - +
73B GLN* 3.5 31.8 + - + +
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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
----------------------------------------------------------
60B THR* 3.7 29.4 - - - -
61B GLU 3.7 9.6 - - - +
62B SER* 4.6 7.4 + - - +
71B TYR* 1.3 84.1 + - - +
73B GLN* 1.3 64.6 + - - +
74B ASN* 3.8 14.5 + - - +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 3.9 13.9 - - - +
154A LYS* 3.4 26.6 - - - +
155A GLU* 2.5 37.1 + - - +
60B THR* 3.5 2.4 - - - -
61B GLU* 2.8 43.0 + - + +
63B ARG* 4.6 9.2 - - + +
71B TYR* 3.5 26.7 + - + -
72B THR* 1.3 70.8 - - - +
74B ASN* 1.3 70.0 + - - +
75B TYR* 3.5 36.4 - - + +
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Residues in contact with ASN 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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128A GLU* 4.8 7.3 + - - +
153A LYS 4.0 0.6 - - - +
154A LYS* 3.9 0.9 - - - -
155A GLU* 3.3 59.2 + - + +
59B TRP 4.0 3.2 - - - +
60B THR* 3.8 19.6 - - - -
72B THR* 3.8 12.7 + - - +
73B GLN* 1.3 82.9 + - - +
75B TYR* 1.3 63.5 + - - +
76B THR* 6.0 0.7 - - - +
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Residues in contact with TYR 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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10A THR* 6.1 4.0 - - + -
11A ILE 5.0 3.8 - - - -
152A LEU* 4.7 11.9 - - + -
153A LYS 3.5 4.3 - - - -
154A LYS* 3.4 53.5 + - + -
58B ARG* 3.6 2.1 - - - +
59B TRP* 3.0 77.9 + + + +
61B GLU* 3.7 20.6 - - + -
63B ARG* 4.1 12.0 + - - -
73B GLN* 3.5 32.6 - - + +
74B ASN* 1.3 74.4 - - - +
76B THR* 1.3 67.8 + - - +
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Residues in contact with THR 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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151A LYS 4.0 0.2 - - - +
152A LEU* 3.3 6.4 - - - +
153A LYS* 2.6 63.1 + - - +
56B LYS* 3.6 31.1 + - - -
57B VAL 3.3 12.6 - - - +
58B ARG* 4.2 9.3 - - + +
59B TRP* 4.2 0.7 - - - -
74B ASN* 6.0 0.5 - - - +
75B TYR* 1.3 79.1 + - - +
77B GLU* 1.3 63.7 + - - +
78B GLU* 4.1 18.5 - - + +
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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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9A LEU* 4.6 20.3 + - + +
150A VAL* 4.8 14.3 - - + +
151A LYS 3.3 13.0 - - - +
152A LEU* 4.2 7.8 - - + +
55B ALA 3.7 0.3 - - - +
56B LYS* 3.2 4.0 - - - -
57B VAL* 2.9 40.3 + - + +
59B TRP* 3.8 21.9 - - + -
76B THR* 1.3 75.1 - - - +
78B GLU* 1.3 62.8 + - - +
79B VAL* 5.8 3.1 - - + -
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Residues in contact with GLU 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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139A LYS* 3.0 40.4 + - - -
149A PRO 4.0 0.2 - - - +
150A VAL* 3.4 4.0 - - - +
151A LYS* 2.7 55.1 + - + +
153A LYS* 4.0 18.0 + - + -
52B ARG* 4.6 3.6 + - - -
54B HIS* 4.0 25.1 + - + -
55B ALA 3.1 9.0 - - - +
56B LYS* 4.4 9.5 + - + -
76B THR* 4.1 14.9 - - + +
77B GLU* 1.3 79.3 - - - +
79B VAL* 1.3 65.7 + - - +
80B GLU* 4.2 2.8 - - + +
202B PO4 5.4 1.4 + - - -
203B PO4 4.2 7.2 + - - -
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Residues in contact with VAL 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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148A LEU* 3.9 28.0 - - + -
149A PRO 3.4 11.0 - - - +
150A VAL* 4.1 21.3 - - + -
54B HIS* 3.3 3.6 - - - +
55B ALA* 2.9 40.0 + - + +
77B GLU* 5.8 3.8 - - + +
78B GLU* 1.3 78.1 - - - +
80B GLU* 1.3 63.7 + - - +
81B TYR* 3.7 10.9 + - + +
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Residues in contact with GLU 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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148A LEU* 3.4 29.3 - - - +
149A PRO* 3.1 27.1 + - + +
151A LYS* 2.6 42.1 + - + +
52B ARG* 3.1 29.0 + - + +
53B GLY 4.4 0.7 - - - +
54B HIS* 3.8 14.6 - - + -
78B GLU* 4.2 3.8 - - + +
79B VAL* 1.3 71.7 - - - +
81B TYR* 1.3 60.9 + - - +
82B PHE 4.0 3.0 - - - +
83B ASN* 3.3 28.2 - - - +
205B PO4 3.4 12.9 + - - -
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Residues in contact with TYR 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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148A LEU* 3.6 32.5 - - + +
53B GLY 2.8 10.1 + - - +
54B HIS* 3.9 6.3 - - - -
55B ALA* 3.7 34.8 - - + +
79B VAL* 3.7 15.0 - - + +
80B GLU* 1.3 73.4 - - - +
82B PHE* 1.3 62.7 + - + +
119B PRO* 4.9 4.9 - - - +
123B LEU* 4.3 14.5 - - + +
124B ALA* 3.7 35.5 - - + +
134B VAL* 5.0 1.9 - - + +
136B TYR* 4.2 14.1 - - - +
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Residues in contact with PHE 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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51B ALA* 3.8 16.2 - - + -
52B ARG* 3.4 11.5 - - - +
53B GLY 3.1 37.4 + - - +
80B GLU* 3.6 4.4 - - - +
81B TYR* 1.3 81.8 - - - +
83B ASN* 1.3 72.0 + - - +
84B HIS* 3.8 20.0 - + + -
116B PHE* 3.5 41.1 - + - -
117B GLU 3.7 16.8 - - - -
118B LEU* 3.8 12.8 - - + -
119B PRO* 3.5 29.4 - - + -
123B LEU* 4.7 2.9 - - + -
136B TYR* 4.5 15.9 - + + -
156B PHE* 5.2 2.0 - + - -
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Residues in contact with ASN 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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50B HIS* 2.9 29.1 + - - -
51B ALA 3.4 5.5 - - - +
52B ARG* 3.1 23.9 + - - -
80B GLU* 3.3 14.6 - - - +
82B PHE* 1.3 83.9 - - - +
84B HIS* 1.3 71.8 + - - +
85B LYS* 3.8 12.5 - - - +
205B PO4 3.7 20.2 + - - +
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Residues in contact with HIS 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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49B ILE* 4.2 3.2 - - + +
50B HIS* 3.6 1.6 - - - -
51B ALA* 2.8 39.6 + - + +
82B PHE* 3.8 22.2 - + + -
83B ASN* 1.3 80.7 - - - +
85B LYS* 1.3 84.2 + - - +
86B ASP* 4.3 11.4 - - + +
115B SER 5.1 3.6 - - - -
116B PHE* 3.6 31.9 - - + +
117B GLU 6.0 0.4 - - - -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A PO4 3.2 31.6 + - - +
48B LYS* 6.5 0.4 - - + -
49B ILE* 3.5 9.0 - - - +
50B HIS* 3.8 31.4 - - + +
83B ASN* 3.8 15.7 - - - +
84B HIS* 1.3 94.3 + - - +
86B ASP* 1.3 64.2 - - - +
201B PO4 5.4 0.2 - - - -
205B PO4 3.8 10.1 + - - -
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Residues in contact with ASP 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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48B LYS* 3.6 4.0 - - - +
49B ILE* 3.0 52.7 + - + +
84B HIS* 4.3 11.4 - - + -
85B LYS* 1.3 78.8 - - - +
87B ILE* 1.3 66.7 + - - +
88B LEU* 4.2 3.6 - - + -
115B SER 6.2 0.2 - - - +
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Residues in contact with ILE 87 (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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47B LEU 4.1 4.5 - - - +
48B LYS* 4.5 27.1 - - + +
86B ASP* 1.3 78.8 - - - +
88B LEU* 1.3 64.6 + - - +
89B ILE 3.3 25.4 - - - +
90B GLY 3.8 18.6 - - - +
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Residues in contact with LEU 88 (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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34B VAL* 3.6 28.3 - - + -
47B LEU* 2.8 29.3 + - + +
49B ILE* 3.6 30.7 - - + -
86B ASP* 3.7 13.0 - - + +
87B ILE* 1.3 80.2 - - - +
89B ILE* 1.3 65.4 + - - +
112B TYR* 3.6 39.5 - - + +
113B ALA 4.6 9.2 - - - +
114B PHE* 4.7 4.5 - - + -
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Residues in contact with ILE 89 (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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36B LEU* 5.7 0.9 - - + -
44B VAL* 4.2 21.1 - - + +
45B LYS 4.8 0.7 - - - +
46B SER* 3.4 9.9 - - - -
47B LEU* 3.3 43.0 + - + +
87B ILE* 3.3 9.7 - - - +
88B LEU* 1.3 84.8 - - - +
90B GLY* 1.3 69.1 + - - +
103B HIS* 4.3 29.8 - - + +
105B ILE* 4.1 15.9 - - + -
112B TYR* 3.8 38.6 - - + +
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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