Contacts of the helix formed by residues 58 - 71 (chain B) in PDB entry 2AFB
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 ASN 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 4.0 22.6 - - + +
56B PRO* 2.9 30.0 + - + +
57B ASN* 1.3 75.9 - - - +
59B PRO* 1.3 72.3 - - + +
60B LEU* 2.9 24.7 + - - +
61B GLY 3.0 10.7 + - - -
62B ASP* 2.9 31.7 + - - -
80B ARG* 4.2 0.2 - - - +
83B ASN 4.4 11.1 + - - -
84B ARG* 4.5 4.2 - - - +
85B ILE 4.8 1.2 - - - +
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Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 5.8 1.8 - - - +
21A ILE* 3.8 30.7 - - + +
22A PHE* 4.5 9.4 - - + +
91A GLU* 4.9 4.3 - - - +
100A LYS* 4.0 26.2 - - + +
102A VAL* 3.7 22.7 - - + -
58B ASN* 1.3 91.6 - - + +
60B LEU* 1.3 56.5 + - - +
62B ASP* 3.5 12.6 - - + +
63B ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.6 24.2 - - + -
27A PHE* 4.3 3.6 - - + -
89A PHE* 3.4 52.5 - - + -
102A VAL* 4.7 7.6 - - + -
11B LEU* 4.0 12.1 - - + -
31B TYR* 3.6 21.5 - - + +
58B ASN* 2.9 16.6 + - - +
59B PRO* 1.3 75.0 - - + +
61B GLY* 1.3 60.4 + - - +
63B ALA 3.3 0.2 + - - -
64B ALA* 2.9 31.2 + - - +
85B ILE* 3.8 27.5 - - + +
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.7 22.8 - - - +
56B PRO* 3.5 25.8 - - - +
58B ASN* 3.0 10.5 + - - -
60B LEU* 1.3 77.6 - - - +
62B ASP* 1.3 59.7 + - - +
65B ALA* 3.2 23.0 + - - +
80B ARG* 3.5 8.0 + - - -
85B ILE* 4.7 0.4 - - - -
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.4 22.5 - - + -
57B ASN* 5.2 1.4 - - - +
58B ASN* 2.9 19.9 + - - +
59B PRO* 3.5 15.6 - - + +
61B GLY* 1.3 76.4 - - - +
63B ALA* 1.3 57.1 + - - +
65B ALA* 3.4 4.0 + - - +
66B GLY 2.9 23.9 + - - -
69B ARG* 4.7 2.1 + - - -
80B ARG* 3.0 26.2 + - - +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE 4.6 2.2 - - - +
22A PHE* 3.7 32.3 - - - +
31B TYR* 3.3 30.8 - - + +
59B PRO 2.9 21.3 + - - +
60B LEU 3.3 0.9 + - - +
62B ASP* 1.3 71.3 - - - +
64B ALA* 1.3 61.9 + - - +
66B GLY* 3.7 0.3 - - - -
67B HIS* 2.9 30.8 + - - +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.4 10.8 - - + +
31B TYR* 3.5 31.3 - - + -
55B LEU* 4.2 11.2 - - + -
60B LEU 2.9 17.4 + - - +
61B GLY 3.8 4.5 - - - +
63B ALA* 1.3 75.1 - - - +
65B ALA* 1.3 63.4 + - - +
67B HIS* 3.3 3.6 + - - +
68B LEU* 3.1 28.8 + - - +
85B ILE* 3.9 13.9 - - + -
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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
----------------------------------------------------------
55B LEU* 4.2 11.1 - - + +
61B GLY 3.2 14.8 + - - +
62B ASP* 3.7 4.3 - - - +
64B ALA* 1.3 77.8 - - - +
66B GLY* 1.3 57.4 + - - +
68B LEU* 3.3 13.8 + - - +
69B ARG* 3.0 48.1 + - - +
75B THR* 3.7 9.2 - - + +
78B ILE* 4.7 4.9 - - + -
80B ARG* 4.5 13.2 - - - +
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Residues in contact with GLY 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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22A PHE* 4.6 9.6 - - - -
62B ASP 2.9 14.6 + - - -
63B ALA 3.3 3.5 + - - -
64B ALA 3.3 0.2 - - - -
65B ALA* 1.3 75.3 - - - +
67B HIS* 1.3 51.6 + - - +
69B ARG* 3.3 23.2 + - - +
70B LYS* 2.8 34.4 + - - +
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 5.2 0.2 - - + -
30B THR* 3.6 15.4 + - - -
31B TYR* 3.4 37.2 + - + -
63B ALA 2.9 17.6 + - - +
64B ALA 3.5 4.9 - - - +
66B GLY* 1.3 72.0 - - - +
68B LEU* 1.3 65.1 + - - +
70B LYS* 3.3 3.1 + - - +
71B PHE* 3.2 53.2 + + - -
317B PHE* 3.3 40.8 + + - -
340B NI 2.0 47.5 - - + +
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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
----------------------------------------------------------
9B ILE* 3.9 21.1 - - + -
36B ALA* 4.3 6.7 - - + +
51B PHE* 3.7 31.2 - - + -
55B LEU* 5.2 0.2 - - + -
64B ALA 3.1 18.9 + - - +
65B ALA* 3.4 10.5 - - - +
67B HIS* 1.3 76.2 - - - +
69B ARG* 1.3 61.4 + - - +
71B PHE* 3.1 9.2 + - - -
73B VAL* 2.9 49.3 + - + +
75B THR* 4.1 8.3 - - + -
78B ILE* 3.9 20.6 - - + -
317B PHE* 3.8 26.0 - - + -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 4.7 10.7 - - - -
62B ASP 4.7 4.0 + - - -
65B ALA* 3.0 29.9 + - - +
66B GLY* 3.6 25.9 - - - +
68B LEU* 1.3 72.6 - - - +
70B LYS* 1.3 69.3 + - - +
72B GLY* 2.8 14.4 + - - -
73B VAL 3.5 12.1 - - - +
75B THR* 3.6 31.9 + - + +
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLN* 5.5 0.2 + - - -
66B GLY 2.8 21.1 + - - +
67B HIS* 3.4 7.2 - - - +
69B ARG* 1.3 73.9 - - - +
71B PHE* 1.3 80.5 + - + +
72B GLY* 3.2 2.8 + - - -
340B NI 4.5 11.4 - - + -
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Residues in contact with PHE 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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40B ALA* 4.6 8.5 - - + -
43B ALA* 3.5 15.2 - - - +
44B GLN* 3.5 33.8 + - + +
67B HIS* 3.2 45.1 - + - +
68B LEU 3.1 8.6 + - - +
69B ARG 3.1 1.0 - - - -
70B LYS* 1.3 98.2 - - + +
72B GLY* 1.3 59.3 + - - +
73B VAL* 3.4 1.8 - - + -
317B PHE* 3.6 34.5 - + + -
318B VAL 3.4 25.8 - - - -
319B VAL* 3.7 21.8 - - + -
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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