Contacts of the strand formed by residues 58 - 72 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B GLU 4.2 0.2 - - - +
51B MSE 4.2 5.2 - - - +
52B SER 5.2 0.5 + - - -
55B TRP* 3.4 38.5 - - + +
56B PRO* 3.9 5.7 - - - +
57B GLY* 1.3 79.1 + - - +
59B ALA* 1.3 67.0 + - - +
60B HIS* 5.5 5.8 - - + +
240B LEU* 3.6 25.4 - - - +
271B PRO* 5.0 0.6 - - + +
272B SER* 4.2 17.5 + - - -
47C TRP* 3.5 8.8 - - - -
61C SER 3.0 11.7 - - - +
62C LEU* 5.2 2.5 - - + -
86C TYR* 2.6 46.4 + - + +
101C ARG* 4.2 1.6 + - - -
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Residues in contact with ALA 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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43B VAL* 5.0 1.3 - - + -
49B SER* 5.0 5.2 - - - -
50B GLU 3.5 8.7 - - - +
51B MSE 3.3 30.3 - - + -
55B TRP* 5.2 0.9 - - - +
58B GLU* 1.3 82.7 - - - +
60B HIS* 1.3 66.9 + - - +
61B SER* 4.8 1.1 - - - +
47C TRP* 3.9 8.5 - - + -
59C ALA 3.4 5.0 - - - +
60C HIS* 3.6 1.6 - - - -
61C SER* 3.0 39.4 + - - +
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.8 1.6 - - - +
50B GLU* 2.6 57.6 + - + +
55B TRP* 5.6 0.2 - - - +
58B GLU* 5.5 5.4 - - + +
59B ALA* 1.3 77.9 + - - +
61B SER* 1.3 56.8 + - - +
62B LEU* 5.7 2.5 - - + -
96B ILE* 4.5 8.3 - - + -
268B PRO 3.4 24.9 + - - -
269B THR* 4.2 16.8 - - + -
270B TYR 3.6 9.3 + - - -
271B PRO* 4.3 3.4 - - + +
272B SER* 3.9 20.6 - - - -
273B GLY* 4.2 3.3 + - - -
59C ALA 3.6 4.7 - - - -
60C HIS* 3.7 33.0 + + - -
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Residues in contact with SER 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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43B VAL* 3.7 10.9 - - - +
44B ILE* 4.4 19.7 - - - -
47B TRP* 4.4 7.6 - - - -
48B PHE 3.1 9.2 - - - -
49B SER* 2.8 26.0 + - - -
59B ALA 4.5 1.7 + - - -
60B HIS* 1.3 76.8 + - - +
62B LEU* 1.3 66.8 + - - +
58C GLU* 3.2 5.2 - - - -
59C ALA* 2.8 38.6 + - - -
61C SER* 4.4 3.4 + - - -
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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
----------------------------------------------------------
47B TRP* 3.6 5.3 - - - -
48B PHE* 3.0 33.3 + - + +
60B HIS* 6.1 1.6 - - + -
61B SER* 1.3 83.8 - - - +
63B LYS* 1.3 64.2 + - - +
64B VAL* 3.3 2.6 + - - +
81B PHE* 4.5 10.3 - - + -
83B SER* 4.4 9.9 - - - -
86B TYR* 4.1 31.9 - - + -
89B VAL* 3.9 32.3 - - + -
96B ILE* 4.7 16.6 - - + -
99B THR* 4.6 7.2 - - + -
269B THR* 4.7 4.0 - - + -
57C GLY 3.4 13.7 - - - +
58C GLU* 3.8 13.5 - - + -
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Residues in contact with LYS 63 (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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74A ASP* 3.7 26.3 + - - -
46B GLY 5.0 0.2 - - - +
47B TRP* 3.5 50.6 - - + +
62B LEU* 1.3 68.9 - - - +
64B VAL* 1.3 62.5 + - - +
83B SER* 3.3 7.3 - - - -
84B ALA* 2.7 52.9 + - + -
57C GLY* 3.1 23.9 + - - +
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Residues in contact with VAL 64 (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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46B GLY 3.5 21.4 + - - +
47B TRP 3.9 3.6 - - - -
48B PHE* 3.5 35.9 - - + +
62B LEU 3.3 3.1 + - - +
63B LYS* 1.3 78.0 - - - +
65B GLU* 1.3 64.0 + - - +
66B LYS* 3.7 22.9 - - - +
67B VAL* 4.4 9.6 - - + +
81B PHE* 3.9 23.1 - - + -
82B GLN 3.6 6.7 - - - +
84B ALA 4.4 0.2 - - - -
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Residues in contact with GLU 65 (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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63B LYS 3.6 2.2 + - - -
64B VAL* 1.3 74.7 - - - +
66B LYS* 1.3 63.0 - - + +
82B GLN* 2.6 33.6 + - + +
83B SER 4.3 1.3 - - - +
84B ALA* 3.6 32.7 - - + +
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Residues in contact with LYS 66 (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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64B VAL* 3.5 6.4 - - - -
65B GLU* 1.3 88.4 - - + +
67B VAL* 1.3 72.1 + - - +
68B LEU* 3.6 23.3 - - - +
81B PHE* 3.4 0.3 - - - +
82B GLN* 2.5 42.5 + - + +
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Residues in contact with VAL 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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64B VAL* 4.4 9.6 - - + -
66B LYS* 1.3 88.2 - - - +
68B LEU* 1.3 63.6 + - - +
69B PHE* 3.7 16.8 - - - +
70B GLN* 4.9 9.6 - - + +
79B ILE* 5.7 4.9 - - + -
80B VAL 3.7 10.3 - - - +
81B PHE* 3.8 13.5 - - + -
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Residues in contact with LEU 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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66B LYS* 3.6 34.5 + - - +
67B VAL* 1.3 75.7 - - - +
69B PHE* 1.3 65.1 + - - +
80B VAL* 2.9 13.7 + - + +
81B PHE 4.2 5.8 - - - +
82B GLN* 3.3 37.2 - - + +
88B LYS* 3.6 16.4 - - + -
163B PHE* 3.3 46.5 - - + -
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Residues in contact with PHE 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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67B VAL* 3.7 8.2 - - - +
68B LEU* 1.3 78.4 - - - +
70B GLN* 1.3 76.8 + - - +
71B GLY* 3.8 12.1 - - - -
78B VAL* 3.3 26.9 - - + -
79B ILE* 3.8 0.3 - - - +
80B VAL* 2.7 54.8 + - + +
155B MSE 3.7 33.2 - - + -
159B VAL* 3.4 24.2 - - + -
163B PHE* 4.1 15.0 - + + -
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Residues in contact with GLN 70 (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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38B ALA* 3.2 31.3 + - - +
67B VAL* 4.9 9.8 - - + +
69B PHE* 1.3 90.3 - - - +
71B GLY* 1.3 63.7 + - - +
77B ASP* 6.1 2.3 - - + +
78B VAL 3.5 7.6 - - - +
79B ILE* 4.5 20.7 - - + +
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Residues in contact with GLY 71 (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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69B PHE* 3.8 12.3 - - - -
70B GLN* 1.3 81.3 - - - +
72B LYS* 1.3 61.4 + - - -
73B SER 3.7 2.5 - - - -
76B GLN 3.7 0.7 - - - +
77B ASP* 3.5 5.2 - - - +
78B VAL* 3.0 34.3 + - - -
155B MSE 6.5 0.7 - - - -
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Residues in contact with LYS 72 (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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71B GLY* 1.3 72.2 - - - -
73B SER* 1.3 73.6 + - - +
74B ASP* 5.0 0.7 - - - +
76B GLN* 3.7 9.3 - - - +
77B ASP* 4.2 19.0 + - - +
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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