Contacts of the helix formed by residues 84 - 97 (chain I) in PDB entry 5AKF
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 SER 84 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I TYR* 2.7 14.1 + - - +
38I VAL* 5.0 0.5 - - - +
65I VAL* 3.5 14.4 - - - +
67I SER* 3.4 17.0 - - - -
82I VAL* 3.4 6.7 + - - -
83I SER* 1.3 76.2 - - - +
85I LYS* 1.3 65.3 + - - +
86I LYS* 3.3 6.2 + - - +
87I LEU* 2.9 30.5 + - - +
88I TYR* 2.9 21.7 + - - +
5L C 3.6 7.5 + - - -
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Residues in contact with LYS 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I TYR* 3.4 48.1 - - + +
84I SER* 1.3 70.5 - - - +
86I LYS* 1.3 61.6 + - - +
88I TYR* 3.5 0.9 + - - +
89I TYR* 3.1 49.6 + - + -
4L G 2.7 35.6 + - - +
5L C 2.8 22.7 + - - +
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Residues in contact with LYS 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LEU* 2.8 41.0 + - + -
64I ASN* 3.9 10.4 + - - +
65I VAL* 4.3 16.2 - - + -
84I SER* 3.1 7.3 + - - +
85I LYS* 1.3 78.5 - - - +
87I LEU* 1.3 65.6 + - - +
89I TYR* 4.1 3.2 - - - +
90I TYR* 3.1 25.5 + - + +
5L C 5.0 1.7 + - - +
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 3.8 16.4 - - + -
56I MET* 3.8 22.4 - - + -
59I LEU* 4.1 10.1 - - + -
60I ILE* 4.7 7.4 - - + -
63I LEU* 4.0 25.6 - - + -
65I VAL* 4.3 13.0 - - + +
82I VAL* 3.7 33.0 - - + -
84I SER* 2.9 22.8 + - - +
86I LYS* 1.3 73.7 - - - +
88I TYR* 1.3 67.3 + - - +
90I TYR* 3.3 6.3 - - + +
91I PHE* 3.0 39.7 + - + -
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Residues in contact with TYR 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I LEU* 3.7 19.3 + - + +
25I TYR 3.6 31.0 - - - -
26I LYS* 3.7 22.6 + - + +
36I TYR* 3.6 27.4 - + + -
37I ARG 3.8 17.7 - - - -
38I VAL* 3.7 13.4 - - + +
84I SER 2.9 17.3 + - - +
85I LYS 3.7 1.1 - - - +
87I LEU* 1.3 80.2 - - - +
89I TYR* 1.3 92.5 + + - +
91I PHE* 3.3 1.7 + - - +
92I ALA* 2.8 41.8 + - + +
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Residues in contact with TYR 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LYS* 4.0 24.8 + - + +
36I TYR* 4.0 11.6 + + - -
85I LYS* 3.1 52.3 + - + +
86I LYS* 4.3 2.9 - - - +
88I TYR* 1.3 97.8 - + - +
90I TYR* 1.3 56.2 + - - +
92I ALA* 4.2 5.8 - - + -
93I ASN* 2.7 58.2 + - - +
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Residues in contact with TYR 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 4.4 8.7 + - - +
8I SER* 5.1 1.6 - - - -
11I SER* 2.7 35.1 + - - -
59I LEU* 3.9 19.1 - - + +
63I LEU* 4.0 35.7 - - + +
86I LYS* 3.1 16.0 + - + +
87I LEU* 3.3 11.7 - - + +
89I TYR* 1.3 79.2 - - - +
91I PHE* 1.3 82.4 + + - +
93I ASN* 4.0 3.6 - - - +
94I MET* 3.1 30.0 + - + +
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Residues in contact with PHE 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I SER 3.6 23.3 - - - -
14I LEU* 4.0 13.2 - - + -
15I LEU* 4.0 18.9 - - + +
18I ILE* 3.9 25.6 - - + -
24I LEU* 4.0 18.8 - - + -
38I VAL* 3.8 19.3 - - + -
56I MET* 4.2 3.1 - - - -
59I LEU* 3.4 33.4 - - + -
87I LEU* 3.0 38.2 + - + +
88I TYR 4.0 2.5 - - - +
90I TYR* 1.3 82.0 - + - +
92I ALA* 1.3 60.3 + - - +
94I MET* 3.3 8.5 + - - +
95I LEU* 2.8 29.5 + - - +
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Residues in contact with ALA 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I LEU* 3.9 14.7 - - + +
88I TYR* 2.8 41.4 + - + +
89I TYR* 3.9 11.2 - - + +
91I PHE* 1.3 73.4 - - - +
93I ASN* 1.3 63.5 + - - +
95I LEU* 3.3 6.2 + - - +
96I GLU* 3.1 32.6 + - - +
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Residues in contact with ASN 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I TYR* 2.7 46.1 + - - +
90I TYR* 4.0 3.9 - - - +
92I ALA* 1.3 70.3 - - - +
94I MET* 1.3 66.4 + - - +
96I GLU* 3.2 20.3 + - - +
97I ARG* 3.2 29.2 + - - +
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Residues in contact with MET 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I SER* 4.0 5.8 - - - +
11I SER* 3.5 24.2 - - - +
12I ALA* 3.4 38.6 - - + +
15I LEU* 4.0 5.6 - - + -
90I TYR* 3.1 32.3 + - + +
91I PHE* 3.4 11.9 - - - +
93I ASN* 1.3 76.7 - - - +
95I LEU* 1.3 62.1 + - - +
97I ARG* 3.1 17.0 + - - +
98I ILE* 3.2 11.6 + - - -
101I PHE* 3.7 28.6 - - + -
105I GLU* 4.7 7.2 - - - +
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Residues in contact with LEU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 4.0 13.6 - - + +
19I ILE* 3.8 36.8 - - + -
24I LEU* 4.8 11.4 - - + -
91I PHE 2.8 16.5 + - - +
92I ALA* 3.5 10.5 - - - +
93I ASN 3.3 0.2 - - - -
94I MET* 1.3 73.7 - - - +
96I GLU* 1.3 64.1 + - + +
98I ILE* 3.2 46.2 - - + +
99I ARG* 5.6 0.2 + - - -
109I PHE* 5.6 0.2 - - + -
134I LEU* 5.7 4.0 - - + -
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Residues in contact with GLU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I ALA* 3.1 20.8 + - - +
93I ASN* 3.2 20.7 + - - +
95I LEU* 1.3 79.4 - - + +
97I ARG* 1.3 60.7 + - + +
98I ILE 3.2 2.7 + - - -
99I ARG* 4.5 14.0 + - - +
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Residues in contact with ARG 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I ASN* 3.2 16.7 + - - +
94I MET* 3.1 10.9 + - - +
96I GLU* 1.3 79.6 - - + +
98I ILE* 1.3 63.7 + - - +
99I ARG 3.3 2.7 - - - -
100I LEU* 3.1 48.1 + - + +
101I PHE* 3.8 7.9 - - + -
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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