Contacts of the helix formed by residues 102 - 118 (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 ASN 102 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5I GLU 5.9 1.8 - - - +
8I SER* 5.4 1.8 + - - -
100I LEU 3.3 3.1 + - - +
101I PHE* 1.3 70.0 - - - +
103I MET* 1.3 58.7 + - - +
104I ARG* 3.3 14.5 + - - +
105I GLU* 2.9 44.2 + - - +
106I GLN* 2.8 37.1 + - - +
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Residues in contact with MET 103 (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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102I ASN* 1.3 75.6 - - - +
104I ARG* 1.3 64.7 + - - +
106I GLN* 3.2 15.6 + - - +
107I ILE* 2.9 39.8 + - + +
145I LEU* 4.1 28.5 - - + -
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Residues in contact with ARG 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLU* 2.9 44.9 + - - +
6I ASN* 4.0 11.5 + - - +
8I SER* 4.0 11.4 - - - -
9I GLY* 4.5 11.5 - - - +
102I ASN* 3.3 14.9 + - - +
103I MET* 1.3 78.8 - - - +
105I GLU* 1.3 56.5 + - - +
107I ILE* 3.6 6.8 + - - +
108I ALA* 3.1 26.6 + - + +
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Residues in contact with GLU 105 (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* 3.6 41.2 - - - +
9I GLY* 5.2 0.4 - - - -
12I ALA* 3.3 12.8 - - + +
94I MET* 4.7 4.9 - - - +
100I LEU 4.3 1.0 - - - +
101I PHE* 3.4 36.7 - - + -
102I ASN* 2.9 45.7 + - - +
104I ARG* 1.3 75.9 - - + +
106I GLN* 1.3 57.6 + - - +
108I ALA* 4.4 0.2 - - - -
109I PHE* 2.7 38.3 + - - +
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Residues in contact with GLN 106 (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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101I PHE* 2.9 27.9 + - + +
102I ASN* 2.8 28.4 + - - +
103I MET* 3.4 14.0 - - - +
105I GLU* 1.3 76.8 - - - +
107I ILE* 1.3 60.1 + - + +
109I PHE* 3.7 1.2 - - - +
110I ILE* 2.9 39.0 + - + +
141I TRP* 3.3 68.3 - - + +
145I LEU* 4.8 8.4 - - + +
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Residues in contact with ILE 107 (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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103I MET* 2.9 34.4 + - + +
104I ARG* 3.9 5.8 - - - +
106I GLN* 1.3 78.4 - - - +
108I ALA* 1.3 64.8 + - - +
110I ILE* 3.3 6.2 + - - +
111I LYS* 2.9 31.2 + - - +
145I LEU* 4.3 21.1 - - + -
176I THR* 4.0 35.0 - - + +
177I ILE* 4.0 20.8 - - + +
179I SER* 5.2 1.6 - - - +
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Residues in contact with ALA 108 (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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9I GLY* 3.2 31.6 - - - +
12I ALA* 3.7 7.9 - - + -
13I TYR* 3.4 17.4 - - + +
104I ARG* 3.1 18.7 + - + +
105I GLU 3.3 0.2 + - - -
107I ILE* 1.3 78.2 - - - +
109I PHE* 1.3 58.5 + - - +
111I LYS* 3.3 12.0 + - - +
112I GLY 3.0 22.3 + - - -
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Residues in contact with PHE 109 (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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12I ALA* 3.4 23.7 - - + +
15I LEU* 3.9 17.3 - - + -
16I GLY* 3.7 22.8 - - - -
19I ILE* 4.4 12.1 - - + -
98I ILE* 3.6 25.1 - - + -
101I PHE* 4.0 21.8 - + + -
105I GLU 2.7 21.5 + - - +
106I GLN* 3.7 2.5 - - - +
108I ALA* 1.3 71.9 - - - +
110I ILE* 1.3 64.7 + - + +
112I GLY* 3.1 2.3 + - - -
113I LEU* 2.9 34.8 + - + +
134I LEU* 4.2 20.9 - - + -
138I VAL* 4.4 11.9 - - + -
141I TRP* 3.9 16.6 - + - -
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Residues in contact with ILE 110 (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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106I GLN* 2.9 30.8 + - + +
107I ILE* 3.8 3.4 - - - +
109I PHE* 1.3 74.8 - - + +
111I LYS* 1.3 57.5 + - - +
113I LEU* 3.8 5.8 - - - +
114I TYR* 2.9 29.3 + - + +
127I ILE* 4.7 10.3 - - + -
138I VAL* 4.0 21.8 - - + -
141I TRP* 4.0 29.4 - - + -
142I LEU* 4.1 13.7 - - + -
145I LEU* 4.8 3.4 - - + -
173I PHE* 4.4 10.3 - - + -
177I ILE* 3.4 40.4 - - + -
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Residues in contact with LYS 111 (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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13I TYR* 4.0 20.4 - - + -
107I ILE* 2.9 21.7 + - - +
108I ALA* 3.3 14.4 - - - +
110I ILE* 1.3 77.6 - - - +
112I GLY* 1.3 56.4 + - - +
114I TYR* 3.8 1.4 - - - +
115I VAL* 3.0 39.0 + - + +
177I ILE* 2.8 33.6 - - - +
178I LEU* 4.5 19.7 - - + +
179I SER* 3.6 25.5 + - - -
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Residues in contact with GLY 112 (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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13I TYR* 3.6 34.0 - - - -
16I GLY* 3.7 7.0 - - - -
17I LEU* 3.3 15.0 - - - +
108I ALA 3.0 11.3 + - - -
109I PHE 3.1 2.9 + - - -
111I LYS* 1.3 73.1 - - - +
113I LEU* 1.3 63.7 + - - +
115I VAL 3.6 0.2 + - - -
116I ALA* 3.1 20.1 + - - +
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Residues in contact with LEU 113 (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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16I GLY* 3.7 16.2 - - - +
19I ILE* 4.4 16.2 - - + -
20I GLY* 4.3 4.7 - - - -
109I PHE* 2.9 28.9 + - + +
110I ILE* 3.8 5.4 - - - +
112I GLY* 1.3 75.1 - - - +
114I TYR* 1.3 58.7 + - - +
116I ALA* 4.6 0.4 - - - +
117I GLU* 2.7 48.5 + - + +
118I GLY 3.7 0.2 + - - -
127I ILE* 3.8 28.6 - - + +
129I ASN* 4.7 4.9 - - - +
134I LEU* 4.7 7.9 - - + -
135I LEU* 4.7 8.3 - - + -
138I VAL* 4.1 26.0 - - + -
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Residues in contact with TYR 114 (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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110I ILE* 2.9 18.8 + - + +
111I LYS 3.8 2.7 - - - +
113I LEU* 1.3 73.8 - - - +
115I VAL* 1.3 62.9 + - - +
116I ALA 3.1 1.1 - - - -
118I GLY* 2.6 30.4 + - - +
119I ASP 2.8 38.1 + - - -
120I MET* 3.7 14.5 - - - +
122I LEU* 3.9 13.5 - - + -
125I LEU* 3.2 17.8 - - + +
126I ARG 3.2 35.8 + - - -
127I ILE* 3.4 28.0 - - + +
165I ILE* 4.2 4.0 - - + -
173I PHE* 3.9 19.3 - + + -
178I LEU* 4.0 24.0 - - + -
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Residues in contact with VAL 115 (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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13I TYR* 4.1 18.8 - - + +
17I LEU* 4.0 17.7 - - + -
21I ASP* 4.8 0.9 - - - +
47I LEU* 6.0 7.4 - - + -
51I HIS* 5.7 2.7 - - + +
111I LYS* 3.0 27.4 + - + +
112I GLY 3.8 4.0 - - - +
114I TYR* 1.3 75.9 - - - +
116I ALA* 1.3 59.5 + - - +
118I GLY 4.9 0.2 + - - -
120I MET* 3.9 34.6 - - + +
178I LEU* 5.1 6.7 - - + -
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Residues in contact with ALA 116 (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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16I GLY 4.1 2.2 - - - +
17I LEU* 4.1 10.5 - - + -
20I GLY* 3.7 20.6 - - - -
21I ASP* 3.4 27.8 - - + +
112I GLY 3.1 17.2 + - - +
113I LEU 4.0 1.6 - - - +
114I TYR 3.1 0.8 - - - -
115I VAL* 1.3 79.7 - - - +
117I GLU* 1.3 59.8 + - - +
118I GLY 3.7 0.7 - - - -
1180I MN 2.4 29.6 + - - -
16L C 2.9 6.3 + - - +
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Residues in contact with GLU 117 (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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19I ILE 4.4 0.5 - - - +
20I GLY* 3.1 40.8 - - - +
113I LEU* 2.7 20.0 + - + +
116I ALA* 1.3 75.0 - - - +
118I GLY* 1.3 62.3 + - - +
127I ILE* 4.4 5.6 - - + -
128I TRP* 3.1 46.6 + - - +
129I ASN* 2.8 22.2 + - - -
15K G 3.1 1.9 + - - -
15L C 2.7 51.1 + - - +
16L C 3.6 11.9 + - - +
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Residues in contact with GLY 118 (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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113I LEU 3.7 0.2 + - - -
114I TYR* 2.6 38.7 + - - -
115I VAL 5.4 0.2 - - - +
116I ALA 3.7 0.6 - - - -
117I GLU* 1.3 75.1 - - - +
119I ASP* 1.3 60.9 + - - -
120I MET* 3.2 12.2 + - - +
126I ARG 3.1 13.2 - - - -
127I ILE* 4.3 0.7 - - - -
128I TRP* 3.9 3.1 - - - -
16L C 3.6 17.2 - - - +
17L C 3.6 0.2 + - - -
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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