Contacts of the helix formed by residues 55 - 71 (chain B) in PDB entry 4Q96
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 ARG 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 2.6 30.1 + - - -
14B SER* 3.5 20.2 + - - +
16B LEU* 3.1 30.1 + - - +
51B ALA* 4.1 15.0 - - + +
52B LYS* 2.9 27.3 + - + +
54B ASN* 1.3 99.1 - - - +
56B LYS* 1.3 62.6 + - - +
57B LEU 3.3 1.6 - - - -
58B THR* 3.3 17.6 + - - -
59B PHE* 3.2 33.4 - - - -
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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
----------------------------------------------------------
48B LEU* 2.9 50.3 + - + +
49B ARG 3.0 12.9 + - - -
51B ALA* 3.0 23.0 + - + +
52B LYS 3.6 8.5 - - - +
53B SER* 3.6 16.5 + - - +
54B ASN 3.4 1.8 - - - -
55B ARG* 1.3 75.2 - - - +
57B LEU* 1.3 65.1 + - - +
59B PHE* 3.1 21.8 + - - +
60B LEU 3.8 2.1 + - - -
91B HIS* 3.0 26.9 + - + +
92B VAL* 4.2 13.9 - - + +
95B GLU* 3.7 38.1 - - + -
1615F TYR* 6.0 1.1 - - + -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 3.9 20.9 - - + -
104A LEU* 3.9 28.3 - - + -
107A LEU* 5.2 0.7 - - + -
18B ASN* 5.7 0.4 - - - +
53B SER 4.9 1.4 + - - -
54B ASN 4.7 5.0 + - - +
55B ARG 3.3 0.4 - - - -
56B LYS* 1.3 78.6 - - - +
58B THR* 1.3 62.5 + - - +
60B LEU* 3.0 16.7 + - + +
61B TYR* 3.4 31.9 + - + -
92B VAL* 4.6 7.0 - - - +
1615F TYR* 4.0 20.3 - - + -
1616F SER 3.8 8.7 - - - +
1618F THR 3.6 40.2 - - - +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.7 22.2 - - + -
17B SER 3.4 26.0 - - - +
18B ASN* 2.9 35.4 + - - +
23B VAL* 4.0 12.8 - - + -
54B ASN 4.9 2.6 + - - -
55B ARG* 3.3 18.1 + - - -
56B LYS 3.2 0.4 - - - -
57B LEU* 1.3 77.8 - - - +
59B PHE* 1.3 63.6 + - - +
61B TYR* 3.3 7.5 + - - +
62B LEU* 2.9 20.6 + - - +
1620F PRO* 5.2 0.2 - - + -
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.9 37.0 - - + -
16B LEU* 4.3 8.3 - - + -
44B TRP* 3.1 42.7 + + + +
47B GLU* 3.8 21.1 - - + -
48B LEU* 3.7 36.3 - - + -
51B ALA* 3.9 15.5 - - + -
55B ARG* 3.2 44.4 - - - -
56B LYS* 3.1 14.6 + - - +
58B THR* 1.3 78.9 - - - +
60B LEU* 1.3 57.8 + - - +
62B LEU* 3.2 5.6 + - - +
63B ALA 3.0 22.2 + - - -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.5 31.6 - - + -
107A LEU* 3.9 17.1 - - + +
111A TRP* 5.0 2.6 - - - -
44B TRP* 4.1 24.0 - - + -
48B LEU* 4.7 2.2 - - + -
56B LYS 4.3 2.0 - - - +
57B LEU* 3.0 10.6 + - + +
59B PHE* 1.3 77.9 - - - +
61B TYR* 1.3 56.1 - - - +
63B ALA* 3.1 5.0 + - - +
64B ASN* 2.9 26.9 + - - +
85B LEU* 5.0 2.5 - - + -
88B ALA* 4.2 13.2 - - + -
89B PHE* 4.2 29.6 - - + -
92B VAL* 3.7 31.2 - - + -
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 3.5 24.6 + - + +
106A ARG* 3.9 9.3 + - - +
107A LEU* 3.6 32.7 - - + +
18B ASN* 5.7 0.2 - - - -
20B GLN* 5.8 0.9 - - - +
23B VAL* 3.8 12.8 - - + +
57B LEU* 3.6 39.3 - - + -
58B THR* 3.3 7.9 + - - +
60B LEU* 1.3 73.3 - - - +
62B LEU* 1.3 64.8 + - - +
64B ASN* 3.4 12.2 + - - +
65B ASP* 3.1 17.8 + - - +
204D UNX 4.0 18.8 - - - -
1619F SER* 3.4 25.7 - - - -
1620F PRO* 3.5 35.4 - - + -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.8 19.5 - - + -
16B LEU* 4.1 12.3 - - + -
23B VAL* 3.7 33.3 - - + +
26B LEU* 3.7 29.6 - - + -
27B SER* 4.0 11.2 - - - +
30B LEU* 4.4 5.8 - - + -
44B TRP* 4.0 13.9 - - + +
58B THR 2.9 14.4 + - - +
59B PHE* 3.3 9.9 - - - +
61B TYR* 1.3 73.9 - - - +
63B ALA* 1.3 66.2 + - - +
65B ASP* 3.2 1.9 + - - +
66B VAL* 3.0 38.4 + - + +
81B PHE* 6.1 0.7 - - + -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TRP* 5.3 1.8 - - + -
44B TRP* 3.8 10.5 - - + +
59B PHE 3.0 12.6 + - - +
60B LEU* 3.1 9.6 + - + +
62B LEU* 1.3 76.0 - - - +
64B ASN* 1.3 57.4 + - - +
67B ILE* 2.8 43.3 + - + +
81B PHE* 3.5 40.4 - - + -
85B LEU* 4.8 6.1 - - + -
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Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.6 28.4 - - + +
110A ILE* 4.8 5.6 - - - +
111A TRP* 2.8 35.9 + - + +
60B LEU 2.9 13.4 + - - +
61B TYR* 3.4 14.4 + - - +
63B ALA* 1.3 77.3 - - - +
65B ASP* 1.3 65.3 + - - +
67B ILE* 4.0 0.8 - - - +
68B GLN* 3.0 49.5 + - - +
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Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 4.0 6.2 + - - -
23B VAL* 3.9 10.9 - - + +
24B GLN* 3.2 38.1 + - - +
27B SER* 2.6 29.7 + - - +
31B ILE* 5.0 0.2 - - - +
61B TYR 3.1 14.3 + - - +
62B LEU 3.7 6.3 - - - +
64B ASN* 1.3 78.7 - - - +
66B VAL* 1.3 63.0 + - - +
68B GLN* 5.0 1.3 - - - -
69B ASN* 2.9 54.8 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.5 32.5 - - - +
30B LEU* 3.9 20.2 - - + -
31B ILE* 4.3 7.0 - - + +
62B LEU* 3.0 22.1 + - + +
63B ALA* 3.8 2.9 - - - +
65B ASP* 1.3 76.9 - - - +
67B ILE* 1.3 58.5 + - - +
69B ASN 3.7 0.5 - - - -
70B SER* 2.9 33.4 + - - -
77B PHE* 3.6 44.2 - - + -
81B PHE* 3.7 12.6 - - + -
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Residues in contact with ILE 67 (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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111A TRP* 4.2 13.2 - - + +
116A VAL* 3.5 28.5 - - + -
117A TYR* 3.7 20.6 - - + +
63B ALA* 2.8 30.7 + - + +
64B ASN* 4.0 2.7 - - - +
66B VAL* 1.3 72.8 - - - +
68B GLN* 1.3 63.2 + - + +
70B SER* 2.8 21.0 + - - -
71B LYS* 3.1 15.6 - - + +
77B PHE* 4.5 4.9 - - - +
78B THR* 3.7 18.6 - - - +
81B PHE* 3.5 33.7 - - + -
85B LEU* 4.1 10.1 - - + -
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Residues in contact with GLN 68 (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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110A ILE* 3.4 15.4 - - - +
111A TRP* 4.5 3.0 - - - +
114A ARG* 3.1 42.3 + - - +
116A VAL* 4.2 19.8 - - + +
64B ASN* 3.0 47.1 + - - +
65B ASP* 4.3 2.0 - - - +
67B ILE* 1.3 78.6 - - + +
69B ASN* 1.3 66.3 + - - +
70B SER 3.3 0.7 + - - -
71B LYS* 3.6 19.6 + - - +
72B ARG* 4.9 1.0 + - - +
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Residues in contact with ASN 69 (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 GLN* 5.3 3.6 - - - +
31B ILE* 3.5 26.6 - - + +
65B ASP* 2.9 51.4 + - - +
66B VAL 3.7 0.2 - - - -
68B GLN* 1.3 79.6 - - - +
70B SER* 1.3 60.2 + - - +
71B LYS 3.5 0.2 - - - -
72B ARG* 4.1 20.6 - - - +
73B LYS* 4.7 2.3 + - - +
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 4.7 10.5 - - - -
34B ARG* 6.2 1.6 - - - -
66B VAL 2.9 15.3 + - - -
67B ILE* 2.8 18.2 + - - -
68B GLN 3.2 0.4 - - - -
69B ASN* 1.3 76.3 - - - +
71B LYS* 1.3 59.9 + - - +
72B ARG 3.1 3.1 - - - -
73B LYS* 2.8 27.1 + - - +
74B GLY 3.1 17.0 + - - +
77B PHE* 3.5 36.4 - - - +
78B THR* 4.4 4.7 + - - -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG 6.1 0.9 - - - +
115A SER 3.9 12.5 + - - -
116A VAL* 3.5 33.8 + - + +
67B ILE* 3.1 20.2 - - + +
68B GLN* 3.6 14.4 - - - +
69B ASN 3.5 0.8 - - - -
70B SER* 1.3 79.3 + - - +
72B ARG* 1.3 60.7 + - - +
73B LYS 3.1 1.6 + - - -
74B GLY* 3.5 15.7 + - - +
75B PRO* 5.7 4.0 - - - -
78B THR* 3.4 25.9 + - - +
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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
------------------------------------------------------------
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