Contacts of the strand formed by residues 104 - 118 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C ALA* 3.1 2.6 - - - +
22C TYR* 2.8 53.6 + - - +
101C PRO* 5.0 2.7 - - - -
103C ALA* 1.3 76.4 - - - +
105C LYS* 1.3 64.2 + - - -
106C LEU* 5.0 0.7 - - - -
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER* 6.4 0.9 - - - -
20C TYR 3.5 3.8 - - - +
21C ALA* 3.3 23.8 - - + -
104C GLY* 1.3 74.1 - - - -
106C LEU* 1.3 74.3 + - - +
131C TYR 4.3 0.2 - - - +
132C SER* 3.3 11.6 + - - -
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER* 3.2 8.5 - - - -
20C TYR 2.7 39.0 + - - +
22C TYR* 3.9 16.8 - - + +
64C ILE* 3.4 44.2 - - + -
100C LEU* 5.4 3.1 - - + -
101C PRO* 5.5 4.9 - - + -
104C GLY 5.0 0.7 - - - -
105C LYS* 1.3 79.9 - - - +
107C LYS* 1.3 61.0 + - - +
108C CYS* 4.6 1.3 - - - -
130C SER* 4.6 12.3 - - - -
131C TYR* 3.2 22.7 - - - +
132C SER* 3.2 19.7 - - - +
137C ILE* 3.7 24.0 - - + -
138C CYS* 5.8 0.2 - - - -
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Residues in contact with LYS 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PRO* 4.9 11.2 - - + -
18C PHE 3.9 6.3 - - - +
19C SER* 4.5 4.5 - - - +
106C LEU* 1.3 74.0 - - - +
108C CYS* 1.3 66.3 + - - +
109C GLU* 3.2 30.7 + - - +
130C SER* 3.3 1.2 - - - -
131C TYR* 2.8 47.9 + - + +
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Residues in contact with CYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PRO* 3.4 6.4 - - - +
18C PHE* 2.8 65.0 + - + +
20C TYR* 4.6 4.3 - - - -
64C ILE* 3.8 26.9 - - - -
65C GLY* 4.8 0.4 - - - -
106C LEU 4.4 7.9 - - - -
107C LYS* 1.3 79.5 - - - +
109C GLU* 1.3 66.3 + - - +
110C ALA 4.3 0.2 - - - -
128C VAL* 4.2 4.0 - - + -
129C TYR 3.1 6.1 - - - +
130C SER* 3.3 25.6 - - - +
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Residues in contact with GLU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS* 4.8 19.8 + - - -
15C LEU 5.4 1.8 - - - +
17C PRO* 4.4 15.9 - - + -
107C LYS* 3.2 30.9 + - - +
108C CYS* 1.3 80.1 - - - +
110C ALA* 1.3 62.3 + - - +
111C VAL* 5.0 0.2 - - - +
128C VAL* 3.2 2.5 - - - -
129C TYR* 2.8 45.8 + - + +
131C TYR* 3.6 31.6 + - + +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS* 3.9 7.4 - - - +
15C LEU* 3.0 49.3 + - + +
16C PRO 5.5 1.6 + - - +
18C PHE* 4.9 8.9 - - + -
68C SER* 4.9 8.3 - - - +
108C CYS 4.3 0.2 - - - -
109C GLU* 1.3 76.7 - - - +
111C VAL* 1.3 64.9 + - - +
126C MET* 4.5 8.3 - - - -
127C ASP 3.0 11.0 - - - +
128C VAL* 3.9 13.2 - - + +
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLY* 3.2 21.8 - - - +
13C GLN 3.4 7.2 - - - +
14C LYS* 4.6 9.9 - - + -
15C LEU* 4.5 1.8 - - - +
110C ALA* 1.3 79.6 - - - +
112C VAL* 1.3 64.6 + - - +
113C ALA* 2.9 21.2 + - - +
126C MET* 3.5 4.5 - - - +
127C ASP* 2.8 45.7 + - + +
129C TYR* 4.2 13.7 - - + +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 3.4 21.7 - - + +
12C GLY 2.9 18.2 + - - -
13C GLN* 2.9 23.7 + - + +
15C LEU* 4.2 13.5 - - + -
77C ILE* 3.9 26.5 - - + -
111C VAL* 1.3 76.4 - - - +
113C ALA* 1.3 65.4 + - - +
114C ASP* 2.7 24.0 + - - +
115C VAL* 3.9 13.2 - - + -
124C ILE* 4.2 14.6 - - + -
125C ILE 3.6 4.7 - - - +
126C MET* 4.6 6.5 - - - +
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 4.0 7.4 - - - +
12C GLY* 4.6 2.6 + - - +
111C VAL* 2.9 18.8 + - + -
112C VAL* 1.3 69.5 - - - +
114C ASP* 1.3 65.3 + - - +
125C ILE* 3.1 23.3 + - + +
127C ASP* 3.2 28.9 - - + +
160C LYS* 3.9 24.0 - - + +
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Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.5 25.3 - - - +
112C VAL* 2.7 13.5 + - - +
113C ALA* 1.3 80.6 - - - +
115C VAL* 1.3 99.2 + - - +
116C LEU* 3.6 9.6 - - + +
125C ILE* 3.1 32.7 + - + -
155C LYS* 4.5 1.9 - - - +
158C SER* 3.0 31.5 + - - +
159C ASP 5.0 0.3 + - - -
160C LYS* 4.1 10.3 - - + +
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.8 34.5 - - + +
10C ALA* 4.4 6.5 - - + -
11C ILE* 4.3 7.2 - - + +
80C LEU* 6.3 1.1 - - + -
112C VAL* 3.9 16.8 - - + -
114C ASP* 1.3 97.6 + - - +
116C LEU* 1.3 72.2 + - - +
122C VAL* 3.5 24.5 - - + -
123C VAL 3.4 6.3 - - - +
124C ILE* 4.3 13.7 - - + -
125C ILE 4.9 0.2 - - - +
155C LYS* 3.1 26.5 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ASP* 3.6 15.7 - - + +
115C VAL* 1.3 93.6 - - - +
117C ASP* 1.3 56.6 + - - +
118C LYS* 3.9 8.5 + - - -
122C VAL* 2.7 12.8 - - - +
123C VAL* 2.6 57.5 + - + -
125C ILE* 5.3 1.6 - - + -
155C LYS* 4.3 24.7 - - + +
156C ARG 3.3 23.1 - - - +
157C THR* 3.8 7.0 - - - +
158C SER* 3.4 33.2 - - - +
161C VAL* 5.0 5.8 - - + -
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Residues in contact with ASP 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 1.3 74.1 - - - +
118C LYS* 1.3 68.7 + - - +
119C GLY* 3.1 25.3 + - - +
121C GLY 3.6 6.0 - - - +
122C VAL* 4.4 7.6 - - + +
155C LYS* 4.5 12.4 + - - +
156C ARG* 3.3 35.4 + - - +
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 3.9 8.5 + - - -
117C ASP* 1.3 76.0 + - - +
119C GLY* 1.3 51.2 + - - +
120C SER* 2.6 23.2 + - - -
121C GLY 2.9 16.9 + - - +
123C VAL* 4.0 28.5 - - + -
145C PHE* 4.1 12.4 - - + -
156C ARG* 3.0 32.7 + - - +
157C THR* 4.8 7.5 - - - +
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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