Contacts of the strand formed by residues 118 - 129 (chain C) in PDB entry 3DOY
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 ARG 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C THR* 4.1 10.3 - - - +
45C TYR* 3.1 60.2 + - + -
46C LYS 4.2 0.4 - - - -
47C ASN* 3.9 13.2 - - - +
116C GLY 3.9 1.2 + - - +
117C ASP* 1.3 72.1 - - - +
119C LEU* 1.3 57.4 + - - +
120C GLU* 3.2 40.9 + - - +
140C GLN 3.3 9.0 - - - +
141C VAL* 3.8 13.8 - - + +
142C ASP 4.6 3.5 + - - +
47E ASN* 5.1 1.8 - - - +
118E ARG* 6.2 4.7 - - - +
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Residues in contact with LEU 119 (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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45C TYR* 3.1 4.1 - - - -
46C LYS 2.9 40.8 + - - +
48C ILE* 4.1 13.7 - - + -
65C PHE* 4.0 27.1 - - + -
70C ILE* 4.0 13.0 - - + -
113C VAL* 4.0 23.8 - - + -
117C ASP 3.7 2.4 - - - -
118C ARG* 1.3 68.2 - - - +
120C GLU* 1.3 59.7 + - - +
121C TYR* 3.7 35.4 + - + +
139C ALA* 3.9 22.4 - - + -
140C GLN 3.8 2.2 - - - +
141C VAL* 4.2 12.3 - - + -
146C VAL* 5.1 0.9 - - + -
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Residues in contact with GLU 120 (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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34C THR* 4.8 3.7 + - - +
43C VAL* 3.9 16.3 - - + +
44C ALA 3.3 15.0 - - - +
45C TYR* 3.8 5.2 - - + -
118C ARG* 3.2 31.7 + - - +
119C LEU* 1.3 70.9 - - - +
121C TYR* 1.3 62.0 + - - +
122C HIS* 2.5 34.9 + - + +
139C ALA* 3.2 3.4 - - - -
140C GLN* 2.7 51.6 + - - +
142C ASP 6.2 0.4 - - - +
143C GLY 5.8 1.4 + - - -
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Residues in contact with TYR 121 (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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29C LEU* 2.9 27.9 + - - +
30C VAL* 4.2 4.0 - - + -
42C ILE 3.6 1.6 - - - +
43C VAL* 3.3 6.4 - - - +
44C ALA* 2.7 41.6 + - + +
45C TYR* 4.0 4.7 - - - -
46C LYS* 3.6 27.2 - - + +
65C PHE* 5.1 0.5 - - - -
69C LEU 4.6 2.3 + - - -
70C ILE* 3.6 13.0 - - + -
73C GLY* 3.4 24.6 - - - -
74C MET* 3.5 20.6 - - + -
77C SER* 3.3 25.6 - - - +
119C LEU* 3.7 27.8 - - + +
120C GLU* 1.3 73.1 - - - +
122C HIS* 1.3 63.5 + - - +
123C LEU* 3.9 12.3 - - + -
138C THR 3.6 3.1 - - - +
139C ALA* 4.6 5.2 - - + -
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Residues in contact with HIS 122 (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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35C GLU* 5.7 0.7 - - - -
42C ILE 3.8 2.9 - - - -
43C VAL* 3.6 27.2 - - + +
120C GLU* 2.5 43.0 + - + -
121C TYR* 1.3 75.1 - - - +
123C LEU* 1.3 62.3 + - - +
137C GLY* 3.0 6.9 - - - -
138C THR* 2.6 47.8 + - - +
140C GLN* 3.5 33.9 + - + +
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Residues in contact with LEU 123 (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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41C LYS* 3.1 4.9 - - - +
42C ILE* 2.8 48.2 + - + +
74C MET* 3.2 52.3 - - + +
77C SER* 3.5 19.3 - - - -
78C GLY* 4.3 2.2 - - - +
81C LEU* 4.7 0.4 - - - -
121C TYR* 3.9 12.3 - - + -
122C HIS* 1.3 77.3 - - - +
124C GLU* 1.3 60.2 + - - +
135C VAL* 3.3 37.5 - - + -
136C GLY* 3.5 14.6 - - - +
137C GLY 4.5 0.9 - - - +
149C ALA 5.2 0.7 - - - +
151C LEU* 4.4 6.7 - - + -
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Residues in contact with GLU 124 (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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40C GLN 3.0 13.2 - - - +
41C LYS* 4.0 7.0 - - + +
81C LEU* 4.7 1.3 - - - -
123C LEU* 1.3 75.6 - - - +
125C VAL* 1.3 67.3 + - - +
126C LEU* 3.4 20.5 + - + +
135C VAL* 3.0 18.9 - - - +
136C GLY 3.0 27.7 + - - +
137C GLY* 5.5 1.7 - - - -
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Residues in contact with VAL 125 (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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39C ASN* 3.5 35.2 - - - +
40C GLN 2.8 13.2 + - - +
81C LEU* 3.9 16.4 - - + -
124C GLU* 1.3 77.7 - - - +
126C LEU* 1.3 65.1 + - - +
127C LYS* 3.7 25.8 - - - +
128C HIS* 4.2 12.1 - - + -
133C TRP* 4.0 23.1 - - + -
134C GLN 3.9 4.0 - - - +
135C VAL* 4.6 3.8 - - + +
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Residues in contact with LEU 126 (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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124C GLU* 3.4 21.7 + - + +
125C VAL* 1.3 77.1 - - - +
127C LYS* 1.3 59.8 + - - +
134C GLN* 2.6 38.3 + - + +
135C VAL 4.0 5.4 - - - +
136C GLY* 3.8 30.5 - - - +
150C GLU* 4.1 21.8 - - + +
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Residues in contact with LYS 127 (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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125C VAL* 3.5 7.4 - - - +
126C LEU* 1.3 82.1 - - + +
128C HIS* 1.3 65.1 + - - +
129C LYS* 3.8 38.7 - - + +
132C ILE 4.1 0.4 - - - +
133C TRP* 3.6 1.0 - - - -
134C GLN* 2.8 54.4 + - + +
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Residues in contact with HIS 128 (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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39C ASN* 4.6 8.9 + - - -
86C LEU* 4.2 9.1 - - + +
125C VAL* 4.2 7.6 - - + +
127C LYS* 1.3 78.1 - - - +
129C LYS* 1.3 76.3 + - - +
130C GLY* 2.9 31.5 + - - -
132C ILE 3.4 11.4 - - - +
133C TRP* 3.1 53.0 + + + -
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Residues in contact with LYS 129 (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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127C LYS* 3.8 43.9 - - + +
128C HIS* 1.3 83.3 + - - +
130C GLY* 1.3 63.7 + - - +
131C MET 3.3 0.5 + - - -
132C ILE* 3.0 31.6 + - + +
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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