Contacts of the strand formed by residues 104 - 117 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21G ALA* 3.2 2.9 - - - +
22G TYR* 2.9 44.3 + - - -
101G PRO* 5.0 3.4 - - - -
103G ALA* 1.3 77.4 - - - +
105G LYS* 1.3 64.9 + - - -
106G LEU* 5.0 1.8 - - - -
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Residues in contact with LYS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G SER* 6.5 0.7 - - - -
20G TYR 3.8 4.0 - - - -
21G ALA* 3.5 24.0 - - + -
104G GLY* 1.3 73.7 - - - -
106G LEU* 1.3 74.3 + - - +
131G TYR 4.6 0.3 - - - +
132G SER* 4.7 6.9 + - - +
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Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G SER* 3.2 9.6 - - - -
20G TYR 3.0 34.1 + - - +
22G TYR* 4.0 16.2 - - + +
64G ILE* 3.5 48.2 - - + -
100G LEU* 5.4 3.1 - - + -
101G PRO* 5.6 5.4 - - + -
104G GLY* 5.0 0.9 - - - -
105G LYS* 1.3 86.2 - - - +
107G LYS* 1.3 62.2 + - - +
108G CYS* 4.7 1.3 - - - -
130G SER* 4.7 6.1 - - - -
131G TYR 3.3 19.1 - - - +
132G SER* 3.9 4.9 - - - -
137G ILE* 3.7 32.8 - - + -
138G CYS* 5.9 0.2 - - - -
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Residues in contact with LYS 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G PRO* 4.8 12.6 - - + -
18G PHE 3.8 7.9 - - - +
19G SER* 4.4 3.8 - - - -
106G LEU* 1.3 74.7 - - - +
108G CYS* 1.3 63.6 + - - +
109G GLU* 3.3 30.3 + - + +
130G SER* 3.4 0.5 - - - -
131G TYR* 2.8 45.1 + - + +
132G SER 4.2 7.3 + - - +
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Residues in contact with CYS 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G PRO* 3.4 6.9 - - - +
18G PHE* 2.9 72.6 + - + +
20G TYR 4.5 4.3 - - - -
64G ILE* 3.8 17.5 - - - -
65G GLY* 4.8 0.2 - - - -
106G LEU 4.5 8.5 - - - -
107G LYS* 1.3 75.5 - - - +
109G GLU* 1.3 66.7 + - - +
110G ALA 4.2 0.4 - - - -
128G VAL* 4.4 3.6 - - + -
129G TYR 3.2 7.2 - - - +
130G SER* 3.3 25.4 - - - +
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Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU 5.4 1.3 - - - +
17G PRO* 4.3 15.9 - - + -
107G LYS* 3.3 28.5 + - - +
108G CYS* 1.3 80.5 - - - +
110G ALA* 1.3 66.2 + - - +
111G VAL* 4.6 2.5 - - + +
128G VAL* 3.3 2.7 - - - -
129G TYR* 2.8 42.5 + - + +
131G TYR* 3.6 31.1 + - + +
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LYS* 4.4 0.5 - - - +
15G LEU* 3.6 44.3 + - + +
16G PRO 5.2 2.7 + - - +
18G PHE* 4.8 4.4 - - + -
68G SER* 3.5 32.3 - - - +
108G CYS 4.2 1.0 + - - -
109G GLU* 1.3 72.3 - - - +
111G VAL* 1.3 75.0 + - - +
126G MET* 4.9 4.7 - - + -
127G ASP 3.3 9.2 - - - +
128G VAL* 3.9 6.0 - - + +
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Residues in contact with VAL 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G GLY* 6.0 1.1 - - - -
13G GLN 4.0 14.4 - - - +
14G LYS* 4.7 17.9 - - + -
15G LEU* 4.7 1.3 - - - +
109G GLU* 4.6 6.3 - - + +
110G ALA* 1.3 88.0 - - - +
112G VAL* 1.3 70.7 + - - +
113G ALA* 3.0 9.5 + - + +
126G MET* 3.2 7.5 - - - +
127G ASP* 2.7 44.2 + - + +
129G TYR* 5.1 10.8 - - + -
160G LYS* 5.9 3.4 - - - +
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Residues in contact with VAL 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA* 3.3 23.5 - - + +
11G ILE 2.9 16.3 - - - +
12G GLY* 4.1 4.0 - - - -
13G GLN* 3.3 24.9 + - + +
15G LEU* 4.3 8.5 - - + -
77G ILE* 3.8 30.7 - - + -
111G VAL* 1.3 75.1 - - - +
113G ALA* 1.3 61.7 + - - +
114G ASP 3.9 18.2 - - - +
115G VAL* 3.9 15.3 - - + -
124G ILE* 4.5 7.4 - - + -
125G ILE 3.9 4.5 - - - +
126G MET* 3.9 7.6 - - - -
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Residues in contact with ALA 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 3.2 12.3 - - - +
111G VAL* 3.0 13.5 + - + -
112G VAL* 1.3 72.4 - - - +
114G ASP* 1.3 63.8 + - + +
125G ILE* 2.9 24.5 + - + +
127G ASP* 3.2 29.6 - - + +
160G LYS* 4.1 32.1 + - + +
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Residues in contact with ASP 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 3.9 20.3 - - - +
112G VAL* 3.3 3.6 + - - +
113G ALA* 1.3 84.3 - - + +
115G VAL* 1.3 94.7 + - - +
116G LEU* 4.0 2.9 - - - -
125G ILE* 3.1 30.7 + - + +
155G LYS* 2.8 40.0 + - - -
158G SER* 3.0 33.0 + - - +
159G ASP* 5.7 0.2 - - - +
160G LYS* 5.1 1.4 - - + +
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Residues in contact with VAL 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G PHE* 3.5 49.1 - - + +
8G ALA* 6.0 0.3 - - - -
10G ALA* 5.1 2.2 - - + -
11G ILE* 4.9 10.1 - - + +
80G LEU* 5.9 3.1 - - + -
112G VAL* 3.9 18.2 - - + -
114G ASP* 1.3 104.3 + - - +
116G LEU* 1.3 59.4 + - - +
122G VAL* 3.9 14.4 - - + -
123G VAL 3.2 13.7 - - - +
124G ILE* 4.1 14.6 - - + -
152G PHE* 4.1 11.6 - - + -
155G LYS* 4.6 3.1 + - - -
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Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G ASP* 3.9 4.0 - - - +
115G VAL* 1.3 74.4 - - - +
117G ASP* 1.3 59.5 + - - +
118G LYS* 4.8 13.0 - - - +
122G VAL* 3.0 6.5 - - - +
123G VAL* 2.8 46.6 + - + +
125G ILE* 4.5 16.2 - - + -
154G GLY* 6.2 0.7 - - - -
155G LYS* 3.7 28.9 - - + +
156G ARG 3.7 8.5 - - - +
157G THR* 3.5 44.9 - - + +
158G SER* 3.7 15.7 - - - +
161G VAL* 5.2 1.8 - - + -
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Residues in contact with ASP 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G VAL 4.1 0.4 + - - -
116G LEU* 1.3 74.6 - - - +
118G LYS* 1.3 74.1 + - - +
119G GLY* 4.0 5.2 + - - -
122G VAL* 4.0 2.9 - - - -
150G GLY* 3.4 6.2 - - - -
151G GLY* 3.2 25.8 + - - -
152G PHE* 3.4 53.7 + - + +
153G GLY* 4.1 2.9 + - - -
154G GLY* 4.4 8.5 + - - +
155G LYS 4.7 7.4 + - - +
156G ARG* 5.9 2.3 - - - -
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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