Contacts of the strand formed by residues 40 - 53 (chain C) 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 THR 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.7 34.3 - - + -
84B ALA* 4.3 4.9 - - + -
104B LYS* 3.9 5.8 - - + +
8C ARG 3.3 11.9 - - - +
9C SER* 2.7 20.6 + - - +
39C GLU* 1.3 70.9 - - - +
41C TYR* 1.3 62.9 + - - +
42C ALA* 4.3 0.4 - - + -
66C TYR 3.8 0.7 - - - +
67C SER* 3.4 4.9 + - - -
68C VAL* 2.9 46.6 + - + +
70C GLN* 2.6 30.8 + - - +
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Residues in contact with TYR 41 (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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74A TRP* 3.9 22.7 - + - -
6C TYR* 3.8 18.8 - + - -
7C ALA* 3.2 3.5 - - - -
8C ARG* 2.9 56.1 + - - +
39C GLU* 3.7 6.7 + - + -
40C THR* 1.3 76.5 - - - +
42C ALA* 1.3 61.1 + - - +
43C GLU* 2.5 46.6 + - + +
65C ALA* 3.6 7.5 - - + +
66C TYR 3.3 14.4 - - - -
67C SER* 3.9 12.6 - - - -
82C ARG* 2.8 18.4 + - - -
1F GLC 3.4 36.6 - - - -
2F FRU 5.3 0.2 - - - -
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Residues in contact with ALA 42 (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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62B THR* 6.0 0.7 - - + -
81B PHE* 3.4 36.6 - - + -
84B ALA* 5.2 0.9 - - + -
6C TYR 3.3 9.2 - - - +
7C ALA* 4.0 11.4 - - + -
40C THR 4.3 0.2 - - - -
41C TYR* 1.3 77.0 - - - +
43C GLU* 1.3 62.6 + - - +
44C LEU* 4.1 10.3 - - + -
64C VAL 3.9 0.9 - - - +
65C ALA* 3.2 3.8 - - - +
66C TYR* 2.8 36.7 + - + +
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Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLY* 3.1 22.9 - - - -
6C TYR* 2.7 29.2 + - + +
41C TYR* 2.5 36.0 + - + +
42C ALA* 1.3 73.0 - - - +
44C LEU* 1.3 66.7 + - - +
45C LYS* 3.9 3.4 - - + +
63C ASN* 3.3 31.3 - - - +
64C VAL 3.6 4.0 - - - -
65C ALA* 3.9 4.7 - - + -
82C ARG* 3.3 4.2 + - - -
106C PHE* 3.3 12.9 - - - -
109C ARG* 4.7 1.2 + - - -
421C TRP* 3.6 1.0 - - - -
1F GLC 2.6 32.0 + - - -
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Residues in contact with LEU 44 (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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46B LEU* 4.8 15.3 - - + -
60B PHE* 5.0 0.2 - - + -
62B THR* 4.2 33.4 - - + +
64B VAL* 4.4 15.3 - - + -
81B PHE* 4.6 2.2 - - + -
3C PHE* 4.5 10.3 - - + -
4C HIS 4.0 1.1 - - - -
42C ALA* 4.5 11.9 - - + -
43C GLU* 1.3 79.1 - - - +
45C LYS* 1.3 63.7 + - - +
46C LEU* 4.1 5.0 + - + +
62C THR* 4.8 0.9 + - - -
63C ASN* 3.7 1.4 + - - +
64C VAL* 2.9 36.4 + - + +
66C TYR* 4.3 24.9 - - + +
421C TRP* 4.1 18.6 - - + -
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Residues in contact with LYS 45 (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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2C ASP 3.5 0.4 - - - +
3C PHE* 3.4 10.7 - - - -
4C HIS* 2.7 55.3 + - + +
5C GLY* 4.2 15.0 - - - +
43C GLU* 4.8 3.6 - - - +
44C LEU* 1.3 73.9 - - - +
46C LEU* 1.3 60.6 + - - +
47C GLY 4.2 0.7 - - - -
61C ASP* 2.6 39.8 + - - +
62C THR 3.2 15.5 + - - +
63C ASN* 3.7 24.2 - - - +
83C GLU* 2.9 23.0 + - - +
106C PHE* 5.9 1.3 - - + -
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Residues in contact with LEU 46 (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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3A PHE* 3.7 36.1 - - + -
44A LEU* 4.8 13.0 - - + -
46A LEU* 4.4 25.4 - - + -
1B VAL* 5.7 1.6 - - + -
46B LEU* 4.4 17.3 - - + -
1C VAL* 3.9 19.1 - - + -
2C ASP 3.3 3.4 - - - +
3C PHE* 4.0 21.5 - - + -
44C LEU* 4.1 4.4 + - + +
45C LYS* 1.3 80.1 - - - +
47C GLY* 1.3 58.8 + - - +
60C PHE* 5.0 0.3 - - - -
61C ASP* 4.1 1.3 - - - -
62C THR* 2.7 42.5 + - - +
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Residues in contact with GLY 47 (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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3A PHE* 4.5 4.7 - - - -
1C VAL* 3.6 3.8 - - - +
2C ASP* 2.7 34.6 + - - +
4C HIS* 6.2 0.2 - - - -
45C LYS 4.2 0.4 - - - -
46C LEU* 1.3 75.9 - - - +
48C GLN* 1.3 63.2 + - - +
59C TYR* 3.6 15.0 - - - -
60C PHE 3.0 13.9 - - - -
61C ASP* 4.0 8.4 + - - -
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Residues in contact with GLN 48 (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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3A PHE* 4.3 18.2 + - + +
421A TRP* 4.1 22.0 + - + +
1C VAL* 2.9 36.3 + - - +
2C ASP* 4.2 3.6 - - - -
47C GLY* 1.3 75.8 - - - +
49C GLU* 1.3 75.7 + - - +
50C VAL* 3.3 19.9 + - + +
59C TYR* 3.6 9.8 - - - -
60C PHE* 2.8 33.6 + - + +
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Residues in contact with GLU 49 (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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2C ASP* 4.5 1.8 + - - +
48C GLN* 1.3 78.2 - - - +
50C VAL* 1.3 60.6 + - - +
51C TRP 3.7 11.4 + - - +
52C LYS* 3.4 36.1 + - + +
57C SER* 3.9 15.5 + - - -
58C PHE 3.6 12.8 - - - +
59C TYR* 3.5 20.4 - - + +
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Residues in contact with VAL 50 (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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361A PRO* 3.5 37.2 - - + -
419A ILE* 4.0 18.6 - - + -
421A TRP* 4.3 18.4 - - + -
48C GLN* 3.3 32.5 + - + +
49C GLU* 1.3 74.4 - - - +
51C TRP* 1.3 63.7 + - - +
58C PHE* 3.0 15.3 + - + +
59C TYR 5.2 0.2 - - - -
60C PHE* 4.3 5.6 - - + -
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Residues in contact with TRP 51 (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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319A ILE* 3.9 28.0 - - + -
353A ALA* 3.4 42.9 + - + -
354A GLY* 4.0 7.4 - - - +
361A PRO* 5.3 0.2 - - + -
49C GLU* 3.4 4.3 + - - +
50C VAL* 1.3 87.0 - - + +
52C LYS* 1.3 64.0 + - - +
53C GLU* 3.4 48.5 + - + +
56C LYS* 3.8 34.8 - - + -
57C SER* 3.2 6.8 - - - -
58C PHE* 3.0 52.6 + + + +
91C LEU* 4.7 2.0 - - + -
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Residues in contact with LYS 52 (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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49C GLU* 3.4 30.6 + - + +
51C TRP* 1.3 79.8 - - - +
53C GLU* 1.3 71.2 + - - +
54C GLY 3.1 24.1 + - - +
55C ASP* 4.6 7.5 - - - +
56C LYS 3.3 10.7 + - - +
57C SER* 4.0 9.3 + - - -
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Residues in contact with GLU 53 (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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51C TRP* 3.4 42.8 + - + +
52C LYS* 1.3 79.0 - - - +
54C GLY* 1.3 65.2 - - - +
55C ASP 3.2 0.3 + - - -
56C LYS* 2.9 30.2 + - + +
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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