Contacts of the strand formed by residues 97 - 114 (chain B) in PDB entry 4EFV
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 ALA 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.2 6.1 - - + -
90B LEU* 4.8 10.1 - - + -
91B THR 3.2 8.3 - - - +
92B MET* 3.6 20.2 - - + -
95B LYS 3.8 2.2 + - - +
96B GLN* 1.3 82.8 + - - +
98B ALA* 1.3 63.6 + - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 4.1 6.3 - - - +
91B THR* 2.8 41.6 + - - -
96B GLN* 3.9 9.6 + - - +
97B ALA* 1.3 76.6 - - - +
99B TRP* 1.3 65.2 + - - +
100B ARG* 3.8 25.4 - - - +
201B PO4 4.4 5.8 - - - +
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Residues in contact with TRP 99 (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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44A ILE* 3.5 42.6 - - + +
45A ASN* 5.2 3.0 - - - +
47A SER* 6.2 0.2 - - - -
49A PHE* 3.9 36.8 - + + -
42B VAL* 3.8 25.8 - - + -
43B ASN 5.2 2.9 - - - -
44B ILE* 4.3 16.8 - - + -
51B GLN* 4.1 5.2 - - - -
88B LYS* 4.0 31.2 - - + +
89B ALA* 3.2 12.1 - - - -
90B LEU* 3.5 43.4 - - + +
98B ALA* 1.3 75.8 - - - +
100B ARG* 1.3 63.1 + - - +
201B PO4 5.0 1.7 + - - -
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 4.0 24.7 - - + +
31B ILE* 6.4 0.2 - - + -
34B LYS* 4.6 0.6 - - - +
36B VAL* 4.2 10.7 - - - +
88B LYS* 4.1 3.6 - - - +
89B ALA* 2.7 37.8 + - - +
91B THR* 3.0 40.6 + - - +
92B MET 3.7 0.8 - - - -
93B ASP* 3.1 45.5 + - - +
96B GLN* 3.2 22.4 + - - +
98B ALA* 3.6 16.5 + - - +
99B TRP* 1.3 79.3 - - - +
101B PHE* 1.3 66.4 + - - +
102B ILE* 3.4 6.5 + - + +
201B PO4 3.1 37.7 + - - +
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Residues in contact with PHE 101 (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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21A TRP* 3.8 36.1 - + - -
52A TYR* 4.0 34.1 - + + -
30B ASP* 3.3 8.0 - - - +
31B ILE* 3.0 50.9 + - + +
86B PHE* 3.9 15.0 - - + -
87B VAL* 3.5 5.2 - - - -
88B LYS* 3.5 54.7 - - + -
100B ARG* 1.3 71.6 - - - +
102B ILE* 1.3 58.8 + - - +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 5.2 0.4 - - + -
28B ALA* 3.7 22.0 - - + -
29B THR 3.6 7.0 - - - +
30B ASP* 4.2 7.6 - - + -
36B VAL* 4.1 14.8 - - + -
38B VAL* 4.0 8.3 - - + -
53B PHE* 3.9 19.1 - - + -
86B PHE* 3.3 9.2 - - - -
87B VAL 2.9 41.7 + - - +
89B ALA* 3.5 20.2 - - + -
91B THR* 4.0 19.5 - - + -
100B ARG* 3.8 9.4 - - + +
101B PHE* 1.3 78.8 - - - +
103B ARG* 1.3 61.8 + - - +
104B ILE* 3.6 15.5 + - + +
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Residues in contact with ARG 103 (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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25B LYS* 5.1 2.3 - - - -
28B ALA* 4.6 6.8 - - - +
29B THR* 2.9 43.3 + - - +
30B ASP 3.4 18.8 + - - -
31B ILE 4.5 8.5 + - - -
33B GLY* 4.6 6.3 - - - +
84B HIS* 3.4 50.3 + - + +
85B THR 3.6 4.9 - - - -
86B PHE* 4.1 18.7 - - + -
102B ILE* 1.3 73.0 - - - +
104B ILE* 1.3 69.1 + - - +
105B ASP* 4.4 3.1 - - - +
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Residues in contact with ILE 104 (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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25B LYS* 4.0 27.8 - - + -
53B PHE* 3.8 27.8 - - + -
54B PHE 3.8 17.9 - - - +
55B GLU* 4.4 11.9 - - + +
84B HIS* 3.9 3.6 - - - -
85B THR* 3.0 29.9 + - + -
87B VAL* 3.8 30.5 - - + -
102B ILE* 4.0 14.1 - - + +
103B ARG* 1.3 83.3 - - - +
105B ASP* 1.3 75.4 + - - +
106B THR* 3.4 6.3 + - + +
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Residues in contact with ASP 105 (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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55B GLU* 3.5 11.4 + - + +
56B THR 3.0 37.0 + - - +
57B LYS* 2.3 31.7 + - - +
82B THR* 3.5 25.0 + - - -
83B THR 3.6 8.0 - - - +
84B HIS* 3.7 16.7 - - - +
103B ARG* 5.1 3.1 - - - +
104B ILE* 1.3 72.9 - - - +
106B THR* 1.3 64.7 + - - +
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Residues in contact with THR 106 (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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83A THR* 5.0 1.6 + - - -
84A HIS 4.6 6.2 - - - +
85A THR* 3.5 25.1 - - - +
106A THR* 3.0 34.6 + - - +
54B PHE* 4.0 7.2 - - + +
56B THR* 3.4 21.5 + - - +
83B THR* 2.9 7.8 + - - -
84B HIS 4.0 1.4 - - - -
85B THR* 3.5 28.2 + - + -
104B ILE* 3.5 11.2 - - + +
105B ASP* 1.3 79.5 - - - +
107B ALA* 1.3 65.1 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 4.4 6.3 - - - +
107A ALA* 3.5 32.8 - - + -
109A VAL* 4.6 4.3 - - + -
17B SER* 4.7 0.7 - - - -
56B THR* 3.9 12.1 - - - -
82B THR* 3.1 9.2 - - - -
83B THR* 2.9 34.7 + - - +
106B THR* 1.3 81.6 + - - +
108B CYS* 1.3 60.6 + - - +
109B VAL* 4.0 5.8 - - + -
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Residues in contact with CYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 4.5 10.2 - - - +
15B CYS* 3.6 34.6 - - + +
16B ASP 4.0 5.6 - - - +
17B SER* 3.4 22.4 + - - +
58B CYS* 2.0 57.7 - - - +
60B ASP 5.5 0.2 - - - -
80B CYS* 3.7 7.9 - - - -
81B THR 3.2 4.3 - - - -
107B ALA* 1.3 73.1 - - - +
109B VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 109 (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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13A SER* 4.4 14.1 - - - +
107A ALA* 4.7 3.4 - - + -
108A CYS 4.3 9.0 - - - +
109A VAL* 4.1 19.5 - - + -
202A CL 3.9 10.8 - - + -
15B CYS* 3.8 4.9 - - - -
81B THR* 2.8 37.0 + - + +
83B THR* 3.9 36.1 - - + +
107B ALA* 4.3 4.9 - - + -
108B CYS* 1.3 79.5 - - - +
110B CYS* 1.3 69.1 + - - +
111B VAL* 3.6 9.9 + - + -
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Residues in contact with CYS 110 (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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13A SER* 4.0 2.9 + - - -
14A VAL* 3.3 47.2 + - + +
202A CL 3.4 7.9 - - + +
14B VAL* 3.5 16.8 - - + -
15B CYS* 3.5 2.9 - - - -
68B CYS* 2.0 52.7 - - - -
71B ILE* 4.1 4.5 - - - -
78B SER* 3.6 15.3 - - - -
79B TYR 3.7 0.2 - - - -
109B VAL* 1.3 75.1 - - - +
111B VAL* 1.3 62.0 + - - +
112B LEU* 4.2 1.6 - - - -
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Residues in contact with VAL 111 (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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11A GLU* 3.6 40.2 - - + +
12A PHE 3.4 8.7 - - - +
13A SER* 5.5 2.9 - - - +
78B SER* 3.2 6.6 - - - -
79B TYR* 3.0 49.6 + - + +
81B THR* 3.7 29.4 - - + -
109B VAL* 4.2 8.5 - - + +
110B CYS* 1.3 75.7 - - - +
112B LEU* 1.3 66.1 + - - +
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Residues in contact with LEU 112 (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 GLY 4.4 0.2 - - - +
11A GLU* 3.3 8.7 - - - +
12A PHE* 2.5 48.6 + - + +
14A VAL* 3.7 23.1 - - + -
69A ARG* 3.3 39.9 - - + +
70A GLY* 3.6 14.4 - - - +
71B ILE* 4.3 15.5 - - + -
76B TRP* 4.0 22.2 - - + -
77B ASN 3.4 4.0 - - - +
78B SER* 3.8 23.3 - - - -
110B CYS* 4.2 1.3 - - - -
111B VAL* 1.3 73.8 - - - +
113B SER* 1.3 62.1 + - - +
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Residues in contact with SER 113 (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 GLY 4.8 6.8 + - - -
11A GLU* 4.8 14.0 - - - +
12A PHE* 6.1 0.2 - - - -
76B TRP* 3.5 5.8 - - - -
77B ASN* 2.6 58.7 + - - +
79B TYR* 5.8 5.4 - - - -
111B VAL 5.4 0.2 - - - -
112B LEU* 1.3 76.6 - - - +
114B LYS* 1.3 69.4 + - - +
115B LYS 3.2 0.3 + - - -
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Residues in contact with LYS 114 (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 GLY 4.9 6.6 + - - +
12A PHE* 5.7 2.6 - - + -
75B HIS* 3.6 38.0 + - - +
76B TRP* 3.5 41.4 - - + -
77B ASN* 4.6 1.6 + - - -
113B SER* 1.3 73.3 + - - +
115B LYS* 1.3 70.4 + - - +
116B ALA* 3.8 0.5 + - - -
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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