Contacts of the strand formed by residues 58 - 72 (chain A) in PDB entry 2Q41
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 GLU 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU 4.4 0.5 - - - +
51A MSE 4.9 3.1 - - - +
52A SER 5.3 0.2 + - - -
55A TRP* 3.3 41.8 - - + +
56A PRO 4.1 5.8 - - - +
57A GLY* 1.3 79.5 + - - +
59A ALA* 1.3 66.3 + - - +
60A HIS* 5.1 8.0 - - + -
240A LEU* 3.7 24.2 - - - +
271A PRO* 5.2 0.7 - - - +
272A SER* 4.1 16.5 + - - -
47D TRP* 3.4 7.7 - - - -
61D SER 3.1 10.3 - - - +
62D LEU* 3.8 12.6 - - + -
86D TYR* 2.5 34.5 + - + -
101D ARG* 4.3 0.9 + - - -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER* 4.8 0.4 - - - -
50A GLU 3.5 17.0 - - - +
51A MSE 3.8 13.9 - - + -
55A TRP* 5.4 1.1 - - - -
58A GLU* 1.3 80.0 - - - +
60A HIS* 1.3 67.7 + - - +
61A SER* 4.0 1.0 + - - +
44D ILE* 4.1 13.7 - - + -
47D TRP* 3.6 16.6 - - + -
59D ALA 3.9 0.2 - - - +
60D HIS* 3.5 3.8 - - - -
61D SER* 2.8 36.6 + - - +
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE 3.8 0.3 - - - +
49A SER* 3.5 0.3 - - - -
50A GLU* 2.8 46.9 + - + +
58A GLU* 5.1 8.0 + - + -
59A ALA* 1.3 77.4 + - - +
61A SER* 1.3 64.1 + - - +
62A LEU* 6.3 0.4 - - + -
96A ILE* 4.9 7.6 - - + +
268A PRO 4.1 10.8 + - - -
269A THR* 4.8 3.4 - - - +
270A TYR 3.1 33.1 + - - -
271A PRO* 4.2 3.6 - - + -
272A SER* 3.4 20.5 + - - -
59D ALA 3.5 2.9 - - - +
60D HIS* 3.2 39.8 - + + -
268D PRO 4.8 6.1 - - - -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TRP* 3.8 16.4 - - - -
48A PHE 3.0 6.3 - - - -
49A SER* 2.8 24.9 + - - -
59A ALA 4.3 1.4 + - - -
60A HIS* 1.3 77.0 - - - +
62A LEU* 1.3 73.1 + - - +
43D VAL* 3.8 12.7 - - - +
44D ILE* 4.5 1.6 - - - +
58D GLU* 3.2 5.0 - - - +
59D ALA* 2.7 39.9 + - - +
61D SER* 4.2 8.8 + - - -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TRP* 3.4 4.3 - - - -
48A PHE* 2.7 42.9 + - + +
60A HIS* 5.7 0.7 - - + -
61A SER* 1.3 84.4 - - - +
63A LYS* 1.3 63.4 + - - +
64A VAL* 3.2 0.9 + - - +
81A PHE* 4.4 17.3 - - + -
83A SER* 4.7 6.1 - - - -
85A THR 6.1 0.2 - - - +
86A TYR* 4.0 25.8 - - + -
89A VAL* 4.2 23.8 - - + -
96A ILE* 4.0 26.5 - - + -
99A THR* 4.6 7.6 - - - +
269A THR* 4.9 6.7 - - + -
57D GLY 3.2 13.9 - - - +
58D GLU* 3.9 12.1 - - + -
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PRO 3.8 7.0 - - - -
46A GLY* 2.9 43.4 + - - +
47A TRP* 3.2 34.4 - - + +
62A LEU* 1.3 69.7 - - - +
64A VAL* 1.3 70.4 + - - +
65A GLU* 5.9 1.1 - - - +
83A SER* 3.5 2.8 - - - -
84A ALA* 2.7 52.3 + - + -
57D GLY* 2.8 18.3 + - - -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 2.7 14.8 + - - +
47A TRP 4.2 1.8 - - - -
48A PHE* 3.6 35.4 - - + +
62A LEU 4.0 0.7 - - - +
63A LYS* 1.3 90.7 + - - +
65A GLU* 1.3 66.6 + - - +
66A LYS* 3.8 24.2 - - - +
67A VAL* 4.3 1.1 - - + +
81A PHE* 4.1 23.3 - - + -
82A GLN 4.0 2.2 - - - -
67C VAL* 3.8 33.4 - - + -
70C GLN* 5.6 1.6 - - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS* 3.6 3.4 + - - +
64A VAL* 1.3 75.6 - - - +
66A LYS* 1.3 62.3 + - + +
82A GLN* 2.6 33.1 + - + +
83A SER 3.2 16.3 - - - +
84A ALA* 4.2 18.0 - - - +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.7 6.2 - - - -
65A GLU* 1.3 86.4 - - + +
67A VAL* 1.3 61.0 + - - +
68A LEU* 3.4 27.1 - - + -
81A PHE* 3.7 2.3 - - - +
82A GLN* 2.9 46.5 + - + +
45C PRO* 6.2 1.3 - - - -
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 4.6 1.6 - - + -
66A LYS* 1.3 76.2 - - - +
68A LEU* 1.3 65.1 + - - +
69A PHE* 3.9 16.2 - - - +
70A GLN* 5.1 6.7 - - + +
79A ILE* 6.0 2.9 - - + -
80A VAL 5.0 1.1 - - - +
81A PHE* 4.3 8.3 - - + -
46C GLY* 3.1 25.1 + - - -
47C TRP 4.9 7.0 - - - +
48C PHE* 5.5 1.3 - - + +
64C VAL* 3.7 37.7 - - + +
66C LYS* 5.7 0.9 - - - -
67C VAL* 3.4 33.0 - - + +
70C GLN* 4.6 4.9 - - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LYS* 3.4 42.5 + - + +
67A VAL* 1.3 77.7 - - - +
69A PHE* 1.3 67.7 + - - +
80A VAL* 3.1 31.1 + - + +
81A PHE 4.3 1.3 - - - -
82A GLN* 3.9 19.1 - - + +
88A LYS* 4.1 25.1 - - + +
163A PHE* 3.5 23.6 - - + -
43C VAL* 5.6 0.2 - - - +
45C PRO* 3.4 36.0 - - + +
46C GLY 3.5 8.7 + - - +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 3.7 6.3 - - - +
68A LEU* 1.3 82.6 - - - +
70A GLN* 1.3 67.1 + - - +
71A GLY* 3.9 11.0 - - - -
78A VAL* 4.6 5.2 - - + -
79A ILE* 3.2 3.6 - - - +
80A VAL* 2.8 38.1 + - + +
155A MSE 3.4 49.1 - - + -
159A VAL* 3.7 28.3 - - + -
163A PHE* 4.3 13.0 - + + -
43B VAL 3.1 28.7 - - - -
44B ILE* 4.1 13.0 - - + -
45B PRO* 4.6 5.6 - - + -
43C VAL* 4.8 8.5 - - + -
47C TRP 4.1 12.6 - - - +
49C SER* 5.6 1.1 - - - -
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 5.1 7.7 - - + +
69A PHE* 1.3 83.0 - - - +
71A GLY* 1.3 62.9 + - - +
77A ASP* 3.7 17.2 + - - +
78A VAL 3.3 4.5 - - - +
79A ILE* 3.1 40.3 - - + +
47C TRP 3.8 6.6 + - - +
48C PHE* 3.2 40.1 - - + -
49C SER* 3.5 26.3 + - - +
70C GLN* 3.6 16.6 - - - +
77C ASP* 5.5 2.2 + - - -
79C ILE* 3.2 18.4 - - - +
94C GLY* 5.4 3.8 - - - -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.9 4.1 - - - -
70A GLN* 1.3 77.7 - - - +
72A LYS* 1.3 57.7 + - - -
77A ASP* 4.3 4.5 - - - -
78A VAL* 2.6 41.6 + - - +
155A MSE 3.5 22.9 - - - +
49C SER* 4.2 5.2 - - - -
51C MSE 3.7 8.5 - - - -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY* 1.3 73.2 - - - -
73A SER* 1.3 74.7 + - - +
75A TYR 6.2 0.2 - - - -
76A GLN 3.4 9.4 - - - +
77A ASP* 3.8 29.2 + - - +
93A ASP* 5.5 2.2 + - - -
49C SER 4.9 0.6 + - - -
51C MSE 3.2 55.2 - - + +
52C SER* 4.0 15.4 + - - +
53C PRO* 4.2 12.8 - - + -
93C ASP 4.3 18.2 + - - -
94C GLY* 5.1 1.8 - - - -
95C VAL* 6.2 0.2 - - - -
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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