Contacts of the strand formed by residues 40 - 53 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG 3.3 12.6 - - - +
9A SER* 2.7 21.1 + - - +
39A GLU* 1.3 72.4 - - - +
41A TYR* 1.3 63.7 + - - +
42A ALA* 5.3 0.2 - - + -
66A TYR 4.4 0.2 - - - -
67A SER* 3.4 4.7 + - - -
68A VAL* 2.9 47.0 + - + +
70A GLN* 2.6 30.7 + - - +
81C PHE* 3.7 33.4 - - + -
84C ALA* 4.3 5.4 - - + -
104C LYS* 3.9 5.5 - - + +
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Residues in contact with TYR 41 (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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6A TYR* 3.9 19.3 - + - -
7A ALA* 3.2 3.5 - - - +
8A ARG* 2.9 56.0 + - - +
39A GLU* 3.8 6.3 + - + -
40A THR* 1.3 75.4 - - - +
42A ALA* 1.3 61.4 + - - +
43A GLU* 2.5 46.4 + - + +
65A ALA* 3.6 7.5 - - + +
66A TYR 3.3 14.6 - - - -
67A SER* 3.9 12.8 - - - -
82A ARG* 2.8 18.2 + - - -
74B TRP* 3.9 22.2 - + - -
1D GLC 3.5 37.5 - - - -
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Residues in contact with ALA 42 (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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6A TYR 3.2 5.4 - - - -
7A ALA* 3.9 14.1 - - + -
40A THR* 5.3 0.2 - - + -
41A TYR* 1.3 78.1 - - - +
43A GLU* 1.3 64.3 + - - +
44A LEU* 4.2 10.8 - - + -
64A VAL 3.9 0.5 - - - +
65A ALA* 3.2 4.3 - - - +
66A TYR* 2.8 35.6 + - + +
62C THR* 6.0 0.4 - - + -
81C PHE* 3.4 35.9 - - + -
84C ALA* 5.3 0.4 - - + -
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Residues in contact with GLU 43 (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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5A GLY* 3.2 23.8 - - - -
6A TYR* 2.7 29.7 + - - +
41A TYR* 2.5 36.4 + - + +
42A ALA* 1.3 75.6 - - - +
44A LEU* 1.3 67.2 + - - +
45A LYS* 3.9 3.5 - - + +
63A ASN* 3.4 23.5 - - - +
64A VAL 3.5 4.3 - - - -
65A ALA* 3.8 4.0 - - + -
82A ARG* 3.3 4.0 + - - -
106A PHE* 3.4 20.1 - - - -
109A ARG* 4.7 1.0 + - - -
421A TRP* 3.6 1.0 - - - -
1D GLC 2.8 28.3 + - - -
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Residues in contact with LEU 44 (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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3A PHE* 4.5 9.9 - - + -
4A HIS 4.0 1.3 - - - -
42A ALA* 4.4 12.3 - - + -
43A GLU* 1.3 81.0 - - - +
45A LYS* 1.3 62.4 + - - +
46A LEU* 4.1 3.9 + - + +
62A THR* 4.8 1.0 + - - -
63A ASN* 3.7 1.4 + - - +
64A VAL* 2.9 36.1 + - + +
66A TYR* 4.3 25.6 - - + +
421A TRP* 4.1 15.7 - - + -
46C LEU* 4.8 15.3 - - + -
60C PHE* 4.9 0.2 - - + -
62C THR* 4.1 34.5 - - + +
64C VAL* 4.3 16.8 - - + -
81C PHE* 4.6 2.2 - - + -
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Residues in contact with LYS 45 (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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2A ASP 3.5 0.4 - - - +
3A PHE* 3.4 11.1 - - - -
4A HIS* 2.7 55.7 + - + +
5A GLY* 4.2 15.7 - - - +
43A GLU* 4.7 3.6 - - - +
44A LEU* 1.3 75.5 - - - +
46A LEU* 1.3 61.1 + - - +
47A GLY 4.1 0.4 - - - -
61A ASP* 2.6 40.9 + - - +
62A THR 3.2 17.3 + - - +
63A ASN* 3.7 21.5 - - - +
83A GLU* 2.9 22.0 + - - +
106A PHE* 5.8 1.8 - - + -
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Residues in contact with LEU 46 (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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1A VAL* 3.9 19.5 - - + -
2A ASP 3.3 3.4 - - - +
3A PHE* 4.0 21.3 - - + -
44A LEU* 4.1 3.8 + - + +
45A LYS* 1.3 80.6 - - - +
47A GLY* 1.3 58.9 + - - +
60A PHE* 5.0 0.3 - - - -
61A ASP* 4.0 1.2 - - - -
62A THR* 2.7 42.5 + - - +
3B PHE* 3.7 36.1 - - + -
44B LEU* 4.9 13.0 - - + -
46B LEU* 4.4 21.8 - - + -
1C VAL* 5.7 1.3 - - + -
46C LEU* 4.4 22.7 - - + -
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A VAL* 3.6 4.0 - - - +
2A ASP* 2.7 35.2 + - - +
45A LYS 4.1 0.6 - - - -
46A LEU* 1.3 75.4 - - - +
48A GLN* 1.3 62.3 + - - +
59A TYR* 3.7 15.5 - - - -
60A PHE* 3.1 14.6 - - - -
61A ASP* 4.0 7.8 + - - -
3B PHE* 4.5 4.9 - - - -
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A VAL* 3.0 36.2 + - - +
2A ASP* 4.2 3.4 - - - -
47A GLY* 1.3 73.5 - - - +
49A GLU* 1.3 72.5 + - - +
50A VAL* 3.2 21.4 + - + +
59A TYR* 3.6 9.4 - - - -
60A PHE* 2.9 34.8 + - + +
3B PHE* 4.3 20.4 + - + +
421B TRP* 4.1 22.2 + - + +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ASP* 4.5 2.0 + - - +
48A GLN* 1.3 78.9 - - - +
50A VAL* 1.3 60.6 + - - +
51A TRP 4.0 11.4 - - - +
52A LYS* 3.4 35.5 + - + +
57A SER* 3.9 14.9 + - - -
58A PHE 3.6 11.9 - - - +
59A TYR* 3.6 21.0 - - + +
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Residues in contact with VAL 50 (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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48A GLN* 3.2 32.5 + - + +
49A GLU* 1.3 74.8 - - - +
51A TRP* 1.3 63.0 + - - +
58A PHE* 3.0 15.1 + - + +
59A TYR 5.2 0.2 - - - -
60A PHE* 4.3 6.3 - - + +
361B PRO* 3.5 36.5 - - + +
419B ILE* 4.0 18.8 - - + -
421B TRP* 4.4 17.9 - - + -
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Residues in contact with TRP 51 (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 GLU* 3.4 3.3 + - - +
50A VAL* 1.3 86.2 - - + +
52A LYS* 1.3 67.0 + - - +
53A GLU* 3.4 47.2 + - + -
56A LYS* 3.7 34.5 - - + -
57A SER* 3.2 6.5 - - - -
58A PHE* 3.0 52.4 + + + +
91A LEU* 4.7 1.8 - - + -
319B ILE* 3.9 28.5 - - + -
353B ALA* 3.5 42.7 + - + -
354B GLY* 4.1 7.0 - - - +
361B PRO* 5.3 0.4 - - + -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.4 30.1 + - + +
51A TRP* 1.3 80.7 - - - +
53A GLU* 1.3 72.2 + - - +
54A GLY 3.1 22.2 + - - +
55A ASP* 4.6 6.7 - - - +
56A LYS 3.3 9.0 - - - +
57A SER* 4.1 11.0 + - - -
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Residues in contact with GLU 53 (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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51A TRP* 3.4 42.4 + - + +
52A LYS* 1.3 78.6 - - - +
54A GLY* 1.3 64.8 + - - +
55A ASP 3.1 0.7 + - - -
56A LYS* 2.9 34.5 + - + +
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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