Contacts of the strand formed by residues 104 - 118 (chain F) in PDB entry 1S9C
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 GLY 104 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F ALA* 3.1 2.6 - - - +
22F TYR* 2.8 52.2 + - - +
101F PRO* 5.0 3.1 - - - -
103F ALA* 1.3 77.6 - - - +
105F LYS* 1.3 63.0 + - - -
106F LEU* 5.0 1.3 - - - -
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Residues in contact with LYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F SER* 6.5 0.7 - - - -
20F TYR 3.8 3.6 - - - -
21F ALA* 3.3 23.8 - - + -
104F GLY* 1.3 74.5 - - - -
106F LEU* 1.3 74.8 + - - +
132F SER* 4.0 15.8 + - - +
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F SER* 3.1 24.4 - - - -
20F TYR 3.0 20.8 + - - +
22F TYR* 3.9 16.4 - - + +
64F ILE* 3.5 42.6 - - + -
100F LEU* 5.4 0.4 - - + -
101F PRO* 5.5 3.6 - - + -
104F GLY* 5.0 0.7 - - - -
105F LYS* 1.3 87.3 - - - +
107F LYS* 1.3 60.3 + - - +
108F CYS* 4.7 1.3 - - - -
130F SER* 4.6 11.7 - - - -
131F TYR 3.2 19.1 - - - +
132F SER* 3.7 6.1 - - - +
137F ILE* 3.4 36.3 - - + -
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Residues in contact with LYS 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F PRO* 5.0 11.2 - - + -
18F PHE 3.9 4.9 - - - +
19F SER* 4.4 4.9 - - - -
106F LEU* 1.3 73.4 - - - +
108F CYS* 1.3 66.4 + - - +
109F GLU* 3.2 29.1 + - + +
130F SER* 3.4 2.1 - - - -
131F TYR* 2.9 45.5 + - + +
132F SER 5.0 3.7 + - - +
133F GLU* 5.3 9.9 - - - +
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Residues in contact with CYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PRO* 3.4 6.8 - - - +
18F PHE* 2.7 77.9 + - + +
20F TYR 4.6 4.0 - - - -
64F ILE* 3.9 15.7 - - - -
65F GLY* 4.8 0.7 - - - -
106F LEU 4.6 6.7 - - - -
107F LYS* 1.3 77.5 - - - +
109F GLU* 1.3 67.5 + - - +
128F VAL* 4.3 3.1 - - + -
129F TYR 3.2 5.8 - - - +
130F SER* 3.5 25.1 - - - +
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Residues in contact with GLU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU 5.7 0.2 - - - -
17F PRO* 4.4 15.5 - - + -
107F LYS* 3.2 30.9 + - + +
108F CYS* 1.3 81.7 - - - +
110F ALA* 1.3 64.0 + - - +
111F VAL* 4.6 3.3 - - + +
127F ASP 3.9 0.2 - - - +
128F VAL* 3.2 4.2 - - - -
129F TYR* 3.0 39.2 + - + +
131F TYR* 3.9 28.3 + - + +
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Residues in contact with ALA 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 4.0 5.0 - - - +
15F LEU* 3.4 52.9 + - + +
16F PRO 5.6 1.3 + - - +
17F PRO* 5.4 1.6 - - - +
18F PHE* 5.1 3.9 - - + -
68F SER* 4.8 13.2 - - - +
109F GLU* 1.3 72.8 - - - +
111F VAL* 1.3 74.2 + - - +
126F MET* 4.5 7.4 - - + -
127F ASP 3.2 9.4 - - - +
128F VAL* 4.1 9.6 - - + +
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Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLY* 4.2 10.8 - - - +
13F GLN 3.7 12.8 - - - +
14F LYS* 5.0 6.1 - - + -
15F LEU* 4.3 1.3 - - - +
109F GLU* 4.6 6.5 - - + +
110F ALA* 1.3 89.8 - - - +
112F VAL* 1.3 73.4 + - - +
113F ALA* 3.3 7.8 + - + +
126F MET* 3.3 6.5 - - - +
127F ASP* 2.8 41.1 + - + +
129F TYR* 4.7 13.0 - - + -
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Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ALA* 3.7 24.0 - - + +
11F ILE* 3.8 0.4 - - - -
12F GLY* 2.9 24.4 + - - -
13F GLN* 3.1 15.4 + - + +
15F LEU* 3.9 27.4 - - + -
111F VAL* 1.3 75.5 - - - +
113F ALA* 1.3 59.0 + - - +
114F ASP 3.2 4.0 + - - +
115F VAL* 4.1 23.3 - - + -
124F ILE* 4.7 22.0 - - + -
125F ILE 3.6 10.8 - - - +
126F MET* 4.6 3.4 - - + +
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Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 3.9 9.2 - - - +
12F GLY* 5.6 0.7 - - - -
111F VAL* 3.3 11.3 + - + +
112F VAL* 1.3 72.0 - - - +
114F ASP* 1.3 65.6 + - - +
125F ILE* 2.9 19.2 + - + +
127F ASP* 3.2 28.0 - - + +
160F LYS* 3.4 31.9 - - + +
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Residues in contact with ASP 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 3.3 15.4 - - - +
112F VAL* 3.2 4.4 + - - +
113F ALA* 1.3 83.8 - - + +
115F VAL* 1.3 89.7 + - - +
116F LEU* 4.2 2.7 - - + -
123F VAL 3.4 1.6 - - - +
124F ILE* 3.8 0.2 - - - -
125F ILE* 2.8 41.6 + - + +
155F LYS* 3.0 26.1 + - - -
158F SER* 2.2 37.4 + - - +
159F ASP* 5.4 0.7 - - - +
160F LYS* 4.2 10.4 - - + +
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ALA 4.6 18.2 - - - +
10F ALA* 4.9 5.4 - - + +
11F ILE* 3.8 24.2 - - + +
112F VAL* 4.1 17.7 - - + -
114F ASP* 1.3 93.1 + - - +
116F LEU* 1.3 61.5 + - - +
117F ASP 4.3 0.5 + - - -
122F VAL* 3.0 39.5 - - + -
123F VAL 3.2 8.3 - - - +
124F ILE* 4.4 9.4 - - + -
152F PHE* 4.4 15.2 - - + -
155F LYS* 4.2 5.7 + - - +
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ASP* 3.7 4.7 - - - +
115F VAL* 1.3 86.2 - - - +
117F ASP* 1.3 63.5 + - - +
118F LYS* 3.2 2.8 + - + -
122F VAL* 2.9 12.0 - - - +
123F VAL* 2.6 63.7 + - + +
125F ILE* 4.3 10.8 - - + -
155F LYS* 3.7 27.4 - - + +
156F ARG 4.8 3.8 - - - +
157F THR* 4.2 9.6 - - - -
158F SER* 3.4 39.0 - - - +
161F VAL* 4.5 3.8 - - + -
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Residues in contact with ASP 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F VAL 4.3 0.2 + - - -
116F LEU* 1.3 71.1 - - - +
118F LYS* 1.3 61.9 + - - +
119F GLY* 4.1 10.9 + - - +
121F GLY 4.3 1.6 - - - -
122F VAL* 4.3 4.2 - - - +
150F GLY* 3.5 27.0 - - - +
152F PHE* 3.0 39.0 + - + +
153F GLY* 3.4 25.2 - - - +
154F GLY 4.4 2.5 - - - +
155F LYS* 3.3 21.6 + - - +
156F ARG* 4.6 7.3 - - - +
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Residues in contact with LYS 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 3.2 2.6 + - + -
117F ASP* 1.3 75.6 - - - +
119F GLY* 1.3 64.8 + - - +
120F SER* 3.1 3.3 + - - -
121F GLY 3.1 20.5 + - - +
123F VAL* 4.0 26.5 - - + -
145F PHE* 4.3 16.5 - - + -
156F ARG* 4.8 26.1 + - - +
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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