Contacts of the strand formed by residues 58 - 72 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B TRP* 4.1 7.3 - - - -
61B SER 3.2 7.9 - - - -
62B LEU* 3.8 15.5 - - + -
86B TYR* 2.6 39.7 + - + -
101B ARG* 4.3 1.0 + - - -
50C GLU 4.2 0.3 - - - +
51C MSE 5.0 2.9 - - - +
55C TRP* 3.5 47.7 + - + +
56C PRO 4.2 2.9 - - - +
57C GLY* 1.3 80.5 - - - +
59C ALA* 1.3 67.1 + - - +
240C LEU* 4.0 10.5 - - - +
271C PRO* 4.7 2.3 - - - +
272C SER* 4.0 20.1 + - - -
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 4.4 17.7 - - + -
47B TRP* 4.5 3.1 - - + -
59B ALA 3.4 4.9 - - - +
60B HIS* 3.6 3.3 - - - -
61B SER* 2.8 41.8 + - - +
49C SER* 4.5 1.8 - - - -
50C GLU 3.2 19.1 - - - +
51C MSE 4.2 12.8 - - + -
55C TRP* 5.0 1.8 - - - +
58C GLU* 1.3 80.7 - - - +
60C HIS* 1.3 65.5 + - - +
61C SER* 4.3 0.4 + - - +
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Residues in contact with HIS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA 3.7 2.7 - - - -
60B HIS* 3.7 35.2 + + - -
273B GLY* 6.0 1.1 - - - -
49C SER* 3.1 0.3 - - - -
50C GLU* 2.7 60.0 + - - +
55C TRP* 5.7 0.8 - - - +
59C ALA* 1.3 71.7 - - - +
61C SER* 1.3 64.8 + - - +
62C LEU* 4.7 3.7 - - + +
96C ILE* 4.1 10.8 - - + -
268C PRO 3.6 15.4 + - - -
269C THR* 3.9 8.5 - - + -
270C TYR 3.0 30.3 + - - -
271C PRO* 3.5 11.4 - - + +
272C SER 4.1 4.9 + - - -
273C GLY* 4.8 3.8 - - - -
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 3.5 14.3 - - - +
58B GLU* 3.0 8.0 - - - +
59B ALA* 3.0 39.0 + - - +
61B SER* 4.4 1.9 + - - -
47C TRP* 3.8 15.5 - - - -
48C PHE 3.0 7.6 - - - -
49C SER* 2.3 31.6 + - - -
59C ALA* 4.3 3.1 + - - +
60C HIS* 1.3 76.0 + - - +
62C LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY 3.2 10.8 - - - +
58B GLU* 5.2 2.2 - - + -
47C TRP* 3.3 5.3 - - - -
48C PHE* 2.9 46.3 + - + +
60C HIS* 5.2 1.3 - - + -
61C SER* 1.3 88.5 - - - +
63C LYS* 1.3 59.9 + - - +
64C VAL* 2.9 11.6 + - - +
81C PHE* 4.5 7.6 - - + -
83C SER* 4.0 18.4 - - - -
86C TYR* 4.2 24.9 - - + -
89C VAL* 3.6 29.2 - - + -
96C ILE* 4.4 17.5 - - + -
99C THR* 4.9 2.9 - - - +
269C THR* 5.0 6.7 - - + -
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLY* 3.1 12.5 + - - +
45C PRO 5.3 1.3 - - - +
46C GLY* 3.4 20.9 - - - +
47C TRP* 3.2 36.8 - - + +
62C LEU* 1.3 67.8 - - - +
64C VAL* 1.3 71.7 + - - +
65C GLU* 2.5 31.9 + - - +
84C ALA* 2.9 40.6 + - + +
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Residues in contact with VAL 64 (chain C).
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 34.9 - - + +
46C GLY* 3.0 11.3 + - - +
47C TRP 4.5 1.3 - - - -
48C PHE* 3.8 19.5 - - + +
62C LEU 2.9 17.0 + - - +
63C LYS* 1.3 88.8 + - - +
65C GLU* 1.3 65.0 + - - +
66C LYS* 3.5 19.1 - - - +
70C GLN* 5.9 0.2 - - - +
81C PHE* 3.6 30.1 - - + -
82C GLN 3.8 7.4 - - - +
83C SER* 4.3 3.1 - - - +
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LYS* 2.5 35.9 + - - +
64C VAL* 1.3 75.5 - - - +
66C LYS* 1.3 63.8 + - + +
82C GLN* 2.5 39.7 + - + +
83C SER 3.8 4.7 - - - +
84C ALA* 3.5 23.4 - - - +
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Residues in contact with LYS 66 (chain C).
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* 5.7 0.9 - - - -
64C VAL* 3.5 7.1 - - - +
65C GLU* 1.3 85.7 - - + +
67C VAL* 1.3 64.8 + - - +
68C LEU* 3.8 19.0 + - + -
81C PHE* 3.5 2.8 - - - +
82C GLN* 2.8 50.2 + - + -
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Residues in contact with VAL 67 (chain C).
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* 4.4 0.2 - - - +
46A GLY* 3.1 22.3 + - - -
47A TRP 4.3 11.0 - - - +
64A VAL* 3.8 31.0 - - + -
67A VAL* 3.4 26.2 - - + -
64C VAL* 4.9 0.9 - - + -
66C LYS* 1.3 77.1 - - - +
68C LEU* 1.3 68.5 + - - +
69C PHE 4.0 4.3 - - - +
70C GLN* 2.9 52.0 - - + +
80C VAL 4.7 0.4 - - - +
81C PHE* 4.2 4.5 - - - -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.8 0.2 - - - +
44A ILE 3.9 3.6 - - - +
45A PRO* 2.9 44.1 - - + +
46A GLY 3.3 2.8 + - - -
47A TRP 4.5 1.7 + - - -
66C LYS* 3.8 24.5 - - + -
67C VAL* 1.3 82.4 - - - +
69C PHE* 1.3 62.0 + - - +
80C VAL* 3.0 29.9 + - + +
82C GLN* 4.0 20.0 - - + +
88C LYS* 3.4 40.2 - - + -
163C PHE* 4.1 17.1 - - + -
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 3.6 24.9 - - + -
47A TRP 4.6 3.1 - - - -
51A MSE 5.9 0.2 - - - -
67C VAL* 4.0 0.2 - - - +
68C LEU* 1.3 78.5 - - - +
70C GLN* 1.3 65.9 + - - +
71C GLY* 3.5 25.4 - - - -
78C VAL* 4.1 22.9 - - + -
79C ILE* 3.2 0.5 - - - -
80C VAL* 2.6 38.8 + - + -
155C MSE 3.8 17.5 - - + -
159C VAL* 3.3 50.9 - - + -
163C PHE* 3.8 7.2 - - + -
43D VAL 4.2 7.2 - - - -
44D ILE* 5.0 3.4 - - + -
45D PRO* 3.4 21.1 - - + -
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Residues in contact with GLN 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TRP 3.7 12.3 + - - +
48A PHE* 3.7 18.4 - - + -
49A SER* 3.1 25.7 + - - +
64A VAL* 5.6 2.2 - - - +
67A VAL* 4.6 6.1 - - - +
70A GLN* 3.6 18.9 - - - +
79A ILE* 4.9 6.4 - - - +
64C VAL* 5.9 0.2 - - - +
67C VAL* 2.9 43.8 - - + +
69C PHE* 1.3 84.2 - - - +
71C GLY* 1.3 58.6 + - - +
78C VAL 3.7 4.9 - - - -
79C ILE* 3.5 31.5 - - + +
81C PHE* 4.7 5.5 - - - +
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Residues in contact with GLY 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 6.0 0.2 - - - -
49A SER* 3.8 17.0 - - - -
51A MSE 4.2 6.7 - - - -
69C PHE* 3.5 16.9 - - - -
70C GLN* 1.3 75.7 - - - +
72C LYS* 1.3 66.1 + - - +
77C ASP* 4.1 6.4 - - - +
78C VAL 3.2 24.9 + - - +
44D ILE* 6.1 0.7 - - - -
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Residues in contact with LYS 72 (chain C).
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 5.4 0.2 - - - +
51A MSE 3.0 63.3 + - + +
52A SER* 5.0 4.6 - - - +
53A PRO* 5.4 5.4 - - + -
93A ASP 3.3 24.7 + - - -
94A GLY* 3.6 14.9 - - - -
95A VAL* 6.0 0.8 - - - +
71C GLY* 1.3 75.5 - - - +
73C SER* 1.3 72.4 + - - +
76C GLN 3.8 12.8 - - - +
77C ASP* 4.2 21.3 - - - -
78C VAL 4.4 1.6 - - - +
155C MSE 3.4 10.8 - - - +
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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
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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