Contacts of the strand formed by residues 46 - 63 (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 SER 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.5 9.6 - - - +
45B LYS* 1.3 96.4 + - - +
47B LEU* 1.3 62.2 + - - +
48B LYS* 4.0 27.0 + - - -
89B ILE 3.4 15.5 + - - -
90B GLY 4.7 5.7 - - - -
141B GLU 3.8 0.8 - - - +
142B LEU* 3.8 1.0 - - - -
143B HIS* 2.9 39.3 + - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 5.3 4.7 - - + -
34B VAL* 4.2 23.8 - - + -
36B LEU* 5.0 9.9 - - + -
46B SER* 1.3 75.0 - - - +
48B LYS* 1.3 65.0 + - - +
49B ILE* 6.0 0.4 - - + -
88B LEU* 2.8 41.9 + - + +
89B ILE* 3.3 33.3 + - + +
112B TYR* 3.9 32.1 - - + -
140B ALA* 4.8 1.8 - - + -
141B GLU 3.3 24.5 - - - +
142B LEU* 4.2 17.7 - - + +
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PO4 5.1 6.7 + - - -
45B LYS* 5.4 5.5 - - - +
46B SER* 4.0 22.1 + - - -
47B LEU* 1.3 81.2 - - - +
49B ILE* 1.3 66.0 + - - +
85B LYS* 6.5 0.4 - - + -
86B ASP 3.6 9.4 - - - +
87B ILE* 4.5 29.8 - - + -
140B ALA* 3.5 3.5 - - - +
141B GLU* 2.8 57.2 + - + +
143B HIS* 4.7 14.2 + - + +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.7 26.7 - - + -
47B LEU* 6.0 0.2 - - + -
48B LYS* 1.3 80.2 - - - +
50B HIS* 1.3 62.5 + - - +
51B ALA* 5.7 2.0 - - + +
84B HIS* 5.5 3.6 - - + +
85B LYS* 3.5 6.4 - - - +
86B ASP* 3.0 46.4 + - + +
88B LEU* 3.6 19.5 - - + +
114B PHE* 3.6 35.2 - - + -
115B SER 5.2 1.6 - - - +
116B PHE* 4.7 13.5 - - + -
138B VAL* 4.3 12.1 - - + -
139B LYS 3.2 8.5 - - - +
140B ALA* 4.6 3.8 - - + -
141B GLU* 5.1 0.7 - - - -
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Residues in contact with HIS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PO4 3.4 11.2 - - - -
49B ILE* 1.3 75.5 - - - +
51B ALA* 1.3 74.0 + - - +
52B ARG* 3.2 29.0 + - + -
83B ASN* 2.9 26.6 + - - -
84B HIS 3.6 8.5 - - - -
85B LYS* 3.8 21.3 - - + +
137B TRP* 3.5 8.4 - + - -
138B VAL* 4.4 2.0 - - - -
139B LYS* 2.9 44.4 + - + +
141B GLU* 3.6 17.0 + - - +
201B PO4 2.4 32.5 + - - -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 4.2 2.1 - - + +
50B HIS* 1.3 75.6 - - - +
52B ARG* 1.3 63.0 + - - +
82B PHE* 3.8 14.4 - - + -
83B ASN* 3.4 2.6 - - - -
84B HIS* 2.8 38.2 + - + +
116B PHE* 3.5 40.2 - - + -
137B TRP 3.4 8.5 - - - +
138B VAL* 4.1 3.8 - - + +
156B PHE* 5.4 0.4 - - + -
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 4.0 2.4 - - - +
151A LYS* 3.5 1.0 - - - +
203A PO4 2.9 40.9 + - - -
50B HIS* 3.2 16.1 + - - +
51B ALA* 1.3 77.0 - - - +
53B GLY* 1.3 64.8 + - - +
54B HIS* 3.5 25.8 - - - +
78B GLU* 4.6 2.6 + - - -
80B GLU* 3.1 20.4 + - - -
82B PHE* 3.4 18.8 - - - +
83B ASN* 3.1 16.7 + - - +
135B ARG 4.0 0.7 - - - +
136B TYR* 3.3 3.2 - - - +
137B TRP* 2.9 59.9 + - + +
156B PHE* 5.0 1.1 - - - -
201B PO4 4.4 0.6 + - - -
203B PO4 3.3 17.4 + - - -
205B PO4 3.0 23.8 + - - -
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Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 1.3 77.3 - - - +
54B HIS* 1.3 63.6 + - - +
80B GLU* 3.8 0.9 - - - -
81B TYR* 2.8 27.7 + - - -
82B PHE* 3.1 15.4 + - - +
135B ARG 3.2 9.9 - - - -
136B TYR* 3.4 23.9 - - - -
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Residues in contact with HIS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 3.5 20.4 - - - +
53B GLY* 1.3 74.1 - - - +
55B ALA* 1.3 62.0 + - - +
56B LYS* 3.7 25.1 - - + +
78B GLU* 4.0 23.4 + - + -
79B VAL 3.3 18.4 - - - +
80B GLU* 3.8 12.3 - - + -
81B TYR* 3.9 8.7 - - - -
133B SER 4.0 0.5 - - - +
134B VAL* 3.4 5.3 - - - +
135B ARG* 3.1 34.0 + - - +
136B TYR* 5.1 0.4 - - - -
137B TRP* 3.5 27.1 + + - -
202B PO4 2.8 31.0 + - - -
203B PO4 4.8 1.3 - - - -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B HIS* 1.3 73.3 - - - +
56B LYS* 1.3 61.0 + - - +
57B VAL* 5.7 0.7 - - + -
77B GLU 3.7 0.6 - - - +
78B GLU* 3.1 5.5 - - - +
79B VAL* 2.9 39.8 + - + +
81B TYR* 3.7 23.5 - - + +
133B SER 3.3 9.0 - - - +
134B VAL* 4.0 11.2 - - + -
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 4.4 4.2 - - - +
153A LYS* 4.4 11.5 - - - +
201A PO4 5.1 1.4 + - - -
54B HIS* 3.7 13.5 - - + -
55B ALA* 1.3 76.2 - - - +
57B VAL* 1.3 68.4 + - - +
58B ARG* 4.1 22.0 - - + +
76B THR* 3.6 24.1 - - - +
77B GLU 3.2 8.7 - - - +
78B GLU* 4.4 9.5 + - + -
131B HIS 3.8 0.4 - - - +
132B GLY* 3.5 1.4 - - - -
133B SER* 2.9 44.3 + - - +
135B ARG* 3.7 19.1 - - - +
202B PO4 2.6 41.7 + - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 6.4 0.4 - - + -
56B LYS* 1.3 81.2 - - - +
58B ARG* 1.3 67.9 + - - +
59B TRP* 3.5 19.1 - - + -
76B THR* 3.3 6.4 - - - +
77B GLU* 2.9 43.1 + - + +
131B HIS* 3.1 18.8 - - + +
132B GLY* 4.4 6.1 - - - -
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 2.9 35.1 - - - +
56B LYS* 4.1 21.8 - - + +
57B VAL* 1.3 76.3 - - - +
59B TRP* 1.3 64.1 + - - +
75B TYR 3.6 6.5 - - - +
76B THR* 4.2 11.9 - - - +
130B ARG 5.3 9.1 + - - +
131B HIS* 3.0 39.0 + - - +
135B ARG* 2.9 42.8 - - - +
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Residues in contact with TRP 59 (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* 6.6 0.2 - - + -
152A LEU* 4.0 17.3 - - + -
57B VAL* 3.5 31.4 - - + -
58B ARG* 1.3 77.7 - - - +
60B THR* 1.3 68.5 + - - +
61B GLU* 3.4 26.7 + - + -
73B GLN 4.1 0.3 - - - +
74B ASN* 4.0 1.2 - - - -
75B TYR* 3.0 69.9 + + + +
77B GLU* 3.8 26.9 - - + -
131B HIS* 5.3 5.4 - - + +
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Residues in contact with THR 60 (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 TRP* 1.3 78.6 - - - +
61B GLU* 1.3 70.1 + - - +
72B THR* 3.7 21.3 - - - -
73B GLN 3.5 4.9 - - - -
74B ASN* 3.8 11.2 - - - -
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Residues in contact with GLU 61 (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 TRP* 3.4 27.1 + - + -
60B THR* 1.3 78.9 - - - +
62B SER* 1.3 60.5 + - - +
63B ARG* 2.2 48.3 + - - +
72B THR* 4.2 3.8 - - - +
73B GLN* 2.8 42.0 + - + +
75B TYR* 3.7 12.9 + - + -
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 1.3 71.7 - - - +
63B ARG* 1.3 80.2 + - - +
64B ASN 5.4 1.0 + - - -
70B ALA* 5.3 3.8 - - - +
71B TYR 3.7 10.1 + - - -
72B THR* 4.6 7.7 + - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 2.2 57.4 + - - +
62B SER* 1.3 92.4 + - - +
64B ASN* 1.3 81.8 + - - +
70B ALA* 3.2 14.0 - - - +
71B TYR* 3.1 44.6 + - + +
73B GLN* 4.6 7.3 - - + +
75B TYR* 4.1 13.8 + - - -
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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
------------------------------------------------------------
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