Contacts of the strand formed by residues 56 - 68 (chain B) in PDB entry 1AF6
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 LYS 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B TRP* 3.7 19.6 - - + -
52B LYS* 3.3 3.0 - - - +
53B GLU* 2.9 39.7 + - + +
55B ASP* 1.3 85.8 - - + +
57B SER* 1.3 63.4 + - - +
89B LYS 3.5 4.7 - - - -
90B ASN* 3.1 26.0 + - + +
91B LEU* 4.1 9.3 - - + +
93B GLU* 5.3 13.6 - - - +
319C ILE* 3.8 27.6 - - + -
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Residues in contact with SER 57 (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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49B GLU* 3.9 22.6 + - - -
51B TRP* 3.2 16.5 - - - -
52B LYS* 4.1 12.5 + - - -
55B ASP 4.0 1.6 + - - -
56B LYS* 1.3 76.5 - - - +
58B PHE* 1.3 64.9 + - - +
59B TYR* 5.8 0.5 - - - +
88B GLY* 3.5 3.1 - - - -
89B LYS* 2.8 59.9 + - - +
91B LEU* 4.4 1.4 - - - +
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.5 5.8 - - - +
50B VAL* 3.0 29.7 + - + -
51B TRP* 3.0 35.2 + + + +
57B SER* 1.3 75.6 - - - +
59B TYR* 1.3 59.8 + - - +
86B VAL* 3.7 14.4 - - + -
87B GLN 3.3 3.8 - - - -
88B GLY* 4.1 6.3 - - - -
91B LEU* 3.5 32.3 - - + -
319C ILE* 5.3 1.1 - - + -
351C TRP 4.0 11.2 - - - -
352C GLN* 3.6 26.2 - - - -
353C ALA* 3.7 23.8 - - + -
361C PRO* 3.7 33.9 - - + -
363C ILE* 4.3 12.1 - - + -
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Residues in contact with TYR 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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2B ASP* 2.6 41.3 + - - +
4B HIS* 4.8 5.9 - - - -
47B GLY* 3.6 5.4 - - - -
48B GLN 3.6 6.5 - - - -
49B GLU* 3.5 34.1 - - + +
50B VAL* 5.2 0.4 - - - -
57B SER* 4.2 0.8 - - - +
58B PHE* 1.3 73.4 - - - +
60B PHE* 1.3 75.2 + - - +
61B ASP* 3.9 21.1 + - + -
85B ASN* 3.8 0.9 - - - +
86B VAL* 3.3 6.5 - - - -
87B GLN* 2.9 43.2 + - + +
89B LYS* 3.8 25.4 - - + +
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Residues in contact with PHE 60 (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 LEU 5.0 0.7 - - - -
47B GLY* 3.0 3.8 - - - -
48B GLN* 2.8 38.8 + - + +
50B VAL* 4.3 6.9 - - + +
58B PHE 4.3 0.2 - - - -
59B TYR* 1.3 76.8 - - - +
61B ASP* 1.3 74.4 + - - +
62B THR* 3.4 26.2 - - + -
84B ALA* 4.8 1.3 - - - -
85B ASN 3.6 10.3 - - - -
86B VAL* 4.0 6.5 - - + -
3C PHE* 4.2 13.0 - + - -
7C ALA* 4.1 7.4 - - + -
44C LEU* 5.0 0.7 - - + -
417C MET* 4.0 14.6 - - + -
419C ILE* 3.7 42.2 - - + -
421C TRP* 3.3 49.8 - + - -
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Residues in contact with ASP 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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4B HIS* 6.2 0.2 - - - -
45B LYS* 2.6 40.1 + - - +
46B LEU 4.0 3.6 - - - +
47B GLY* 4.0 11.4 + - - -
59B TYR* 3.9 19.1 + - + -
60B PHE* 1.3 78.2 - - - +
62B THR* 1.3 68.4 + - - +
83B GLU* 4.4 6.2 - - - +
84B ALA* 3.3 5.6 + - - -
85B ASN* 3.1 48.1 + - - +
87B GLN* 4.7 6.2 + - - +
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Residues in contact with THR 62 (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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44B LEU 4.8 1.0 + - - -
45B LYS* 3.2 29.9 + - - +
46B LEU* 2.8 31.8 + - - +
60B PHE* 3.4 36.8 - - + -
61B ASP* 1.3 76.3 + - - +
63B ASN* 1.3 63.9 + - - +
64B VAL* 5.5 0.7 - - - +
81B PHE* 4.8 8.1 - - + -
83B GLU* 3.2 14.4 - - - +
84B ALA* 4.7 2.5 - - + -
3C PHE* 5.1 0.9 - - + -
44C LEU* 4.2 27.4 - - + +
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Residues in contact with ASN 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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43B GLU* 3.3 33.9 - - - +
44B LEU 3.7 6.2 - - - +
45B LYS* 3.7 11.8 - - - +
62B THR* 1.3 79.3 - - - +
64B VAL* 1.3 72.1 + - - +
65B ALA* 4.1 2.6 - - - +
81B PHE* 3.8 4.0 - - - -
82B ARG* 3.0 25.2 + - - -
83B GLU* 2.9 48.4 + - + +
106B PHE* 3.2 23.1 - - - -
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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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42B ALA 3.8 0.9 - - - +
43B GLU* 3.5 0.3 - - - -
44B LEU* 2.9 37.4 + - + +
62B THR* 5.5 0.7 - - - +
63B ASN* 1.3 78.2 - - - +
65B ALA* 1.3 62.5 + - - +
66B TYR* 3.5 36.2 - - + +
79B PRO* 3.8 13.9 - - + -
80B ALA 3.5 6.7 - - - +
81B PHE* 3.8 23.8 - - + -
44C LEU* 4.4 13.9 - - + -
66C TYR* 3.8 24.2 - - + +
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Residues in contact with ALA 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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41B TYR* 3.6 24.2 - - + +
42B ALA 3.2 7.4 - - - +
43B GLU* 3.9 7.2 - - + +
63B ASN* 4.1 0.8 - - - +
64B VAL* 1.3 75.0 - - - +
66B TYR* 1.3 60.3 + - - +
78B ASP 4.6 0.2 - - - +
79B PRO* 3.2 7.4 - - - +
80B ALA* 2.8 35.6 + - - +
82B ARG* 3.7 23.3 - - - -
74C TRP* 4.1 10.9 - - + -
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Residues in contact with TYR 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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64A VAL* 3.8 35.1 - - + +
66A TYR* 4.0 4.0 + - - -
79A PRO* 4.3 6.7 - - + +
81A PHE* 3.8 42.3 - + + -
40B THR 3.8 0.7 - - - +
41B TYR* 3.3 8.4 - - - -
42B ALA 2.8 36.6 + - - +
44B LEU* 4.3 20.2 - - + +
64B VAL* 3.5 37.8 - - + +
65B ALA* 1.3 75.3 - - - +
67B SER* 1.3 61.1 + - - +
68B VAL 4.2 0.4 - - - -
77B THR* 4.1 17.5 - - + -
78B ASP 5.6 0.7 - - - -
79B PRO* 3.6 25.4 - - + +
66C TYR* 4.0 8.3 + - - -
74C TRP* 5.1 0.7 - - - -
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Residues in contact with SER 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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39B GLU* 4.2 15.9 - - - +
40B THR 3.4 7.6 + - - -
41B TYR* 3.9 13.9 - - - -
66B TYR* 1.3 76.6 - - - +
68B VAL* 1.3 66.9 + - - +
77B THR* 3.5 14.4 + - - -
78B ASP 5.6 1.2 + - - -
74C TRP* 4.4 17.9 - - - -
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Residues in contact with VAL 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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81A PHE* 4.2 20.6 - - + +
104A LYS* 4.4 5.8 - - - -
39B GLU* 3.5 7.7 - - - +
40B THR* 2.9 56.1 + - + +
67B SER* 1.3 80.5 - - - +
69B ALA* 1.3 58.5 + - - +
70B GLN 4.3 0.2 - - - +
75B GLU* 3.4 39.0 - - + +
76B ALA 5.1 0.4 - - - +
77B THR* 3.8 29.8 - - + -
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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