Contacts of the strand formed by residues 132 - 141 (chain F) 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 ILE 132 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102F MET* 3.8 28.0 - - + -
128F HIS* 3.3 2.6 - - - -
129F LYS* 2.9 43.2 + - + +
130F GLY 3.2 0.2 - - - -
131F MET* 1.3 81.9 - - + +
133F TRP* 1.3 65.3 + - - +
152F LYS* 3.6 32.8 - - + +
153F ALA 3.7 2.5 - - - -
154F MET* 4.5 12.3 - - + -
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Residues in contact with TRP 133 (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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39F ASN* 3.2 26.9 - - - -
78F GLY 5.5 1.1 - - - +
81F LEU* 4.6 2.2 - - + -
82F ALA* 3.7 37.5 - - + -
85F SER* 3.4 25.4 - - - -
86F LEU* 3.7 19.8 - - + +
125F VAL* 3.7 38.1 - - + -
127F LYS 3.8 1.8 - - - -
128F HIS* 3.4 30.4 + + + +
130F GLY 3.3 20.4 + - - -
131F MET 3.8 8.7 - - - -
132F ILE* 1.3 82.2 - - - +
134F GLN* 1.3 58.7 + - - +
135F VAL* 4.1 13.4 + - + +
151F LEU* 3.8 1.7 - - - +
152F LYS* 3.1 5.8 - - - -
153F ALA* 2.9 40.0 + - + +
155F ILE* 4.8 0.4 - - + -
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Residues in contact with GLN 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F THR* 4.6 5.9 + - - -
125F VAL* 3.9 0.9 - - - +
126F LEU* 2.8 46.2 + - + +
127F LYS* 2.7 44.2 + - + +
132F ILE 4.4 0.2 + - - -
133F TRP* 1.3 72.7 - - - +
135F VAL* 1.3 66.0 + - - +
150F GLU* 5.1 7.3 + - - +
151F LEU* 3.4 12.4 + - - +
152F LYS* 4.1 27.6 - - + +
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Residues in contact with VAL 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F GLY* 4.5 21.1 - - - +
81F LEU* 5.2 4.5 - - + -
123F LEU* 3.8 24.9 - - + -
124F GLU 3.3 17.9 - - - +
125F VAL* 4.1 14.6 - - + -
126F LEU* 3.8 7.8 - - - +
133F TRP* 4.9 13.7 - - + +
134F GLN* 1.3 81.9 - - - +
136F GLY* 1.3 57.8 + - - +
150F GLU* 3.3 3.1 - - - +
151F LEU* 2.7 63.2 + - + +
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Residues in contact with GLY 136 (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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123F LEU* 4.0 8.5 - - - -
124F GLU* 3.0 37.4 + - - +
126F LEU* 3.8 12.9 - - - +
135F VAL* 1.3 79.1 - - - +
137F GLY* 1.3 58.1 + - - -
149F ALA 3.1 12.1 - - - -
150F GLU* 3.9 6.7 - - - -
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Residues in contact with GLY 137 (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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74F MET* 3.8 6.1 - - - -
122F HIS 3.1 11.9 - - - -
123F LEU* 4.1 2.0 - - - +
124F GLU* 5.8 0.9 - - - -
136F GLY* 1.3 75.0 - - - -
138F THR* 1.3 70.0 + - - +
148F GLU* 3.4 1.7 - - - +
149F ALA 2.8 29.6 + - - +
150F GLU* 5.3 0.2 - - - +
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Residues in contact with THR 138 (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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74F MET* 3.8 11.3 - - - +
120F GLU 3.9 0.2 - - - +
121F TYR* 3.8 1.6 - - - -
122F HIS* 2.8 35.7 + - - +
137F GLY* 1.3 81.2 - - - +
139F ALA* 1.3 60.5 + - - +
140F GLN* 3.2 24.6 + - - -
145F VAL* 4.1 24.4 - - + +
147F ALA 3.2 14.1 - - - +
148F GLU* 4.2 9.4 - - + -
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Residues in contact with ALA 139 (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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70F ILE* 3.6 31.9 - - + -
74F MET* 4.1 9.0 - - + -
119F LEU* 4.1 7.6 - - + -
120F GLU 3.2 7.6 - - - +
121F TYR* 4.6 3.6 - - + +
138F THR* 1.3 74.1 - - - +
140F GLN* 1.3 62.5 + - - +
145F VAL* 3.6 0.5 - - - -
146F VAL* 2.8 37.6 + - + -
147F ALA* 2.9 12.6 + - + +
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Residues in contact with GLN 140 (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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118F ARG 3.3 2.6 - - - +
119F LEU 3.7 0.2 - - - -
120F GLU* 2.6 54.3 + - - +
122F HIS* 3.2 33.2 + - + +
138F THR* 3.2 21.9 + - - +
139F ALA* 1.3 79.4 - - - +
141F VAL* 1.3 67.2 + - - +
142F ASP 4.2 0.2 - - - -
143F GLY* 4.0 21.5 - - - +
144F LYS 3.2 14.8 - - - +
145F VAL* 4.0 16.0 - - - +
146F VAL 4.4 0.2 - - - +
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Residues in contact with VAL 141 (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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113F VAL* 4.2 4.5 - - + -
117F ASP* 3.6 42.0 - - + +
118F ARG* 3.8 13.9 - - + +
119F LEU* 4.0 17.9 - - + -
140F GLN* 1.3 78.2 - - - +
142F ASP* 1.3 77.9 + - + +
143F GLY 3.2 0.7 - - - -
144F LYS* 3.0 22.4 + - - +
146F VAL* 3.4 23.8 - - + -
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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