Contacts of the strand formed by residues 115 - 123 (chain F) in PDB entry 3PJV
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 ALA 115 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D VAL* 5.1 1.6 - - + +
38D LEU* 3.6 46.2 - - + +
39D ARG* 3.9 8.5 - - + +
42D ALA* 3.5 5.1 - - - +
113F GLU 3.4 3.7 + - - +
114F PRO* 1.3 71.7 - - - +
116F GLY* 1.3 58.6 + - - +
134F VAL* 3.3 7.9 - - - +
135F SER* 2.9 36.1 + - - +
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Residues in contact with GLY 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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39D ARG* 3.8 24.8 - - - +
42D ALA* 3.8 5.4 - - - -
43D GLN* 5.3 0.2 - - - +
114F PRO* 3.8 5.0 + - - -
115F ALA* 1.3 75.4 - - - +
117F GLY* 1.3 58.7 + - - -
133F VAL 3.2 10.5 - - - -
134F VAL* 4.3 6.5 - - - -
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Residues in contact with GLY 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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42D ALA* 3.7 2.8 - - - +
43D GLN* 3.7 27.1 - - - -
46D ALA* 3.7 8.0 - - - +
116F GLY* 1.3 75.0 - - - -
118F ASP* 1.3 65.0 + - - +
132F GLU* 3.6 1.0 - - - +
133F VAL 2.9 31.8 + - - +
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Residues in contact with ASP 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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43D GLN* 3.0 24.1 + - - +
46D ALA* 3.8 2.2 - - - +
117F GLY* 1.3 77.6 - - - +
119F ALA* 1.3 62.6 + - - +
120F LEU* 6.1 0.7 - - - +
130F ARG* 4.3 22.0 - - + +
131F VAL 3.0 14.6 - - - +
132F GLU* 4.4 6.3 - - + -
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Residues in contact with ALA 119 (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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46D ALA* 3.5 30.0 - - - +
47D THR* 3.8 13.7 - - + +
50D ALA* 3.7 10.1 - - + -
118F ASP* 1.3 78.6 - - - +
120F LEU* 1.3 66.1 + - - +
130F ARG* 3.5 4.0 - - - +
131F VAL* 2.8 33.3 + - + +
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Residues in contact with LEU 120 (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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50D ALA* 3.7 10.9 - - - +
54D THR* 5.3 0.3 + - - -
84D LEU* 4.0 14.1 - - + -
118F ASP* 6.1 0.7 - - - +
119F ALA* 1.3 76.5 - - - +
121F VAL* 1.3 65.2 + - - +
122F SER* 4.1 9.0 + - - +
127F GLN* 3.4 36.1 - - + +
129F ALA 3.5 13.2 - - - +
130F ARG* 3.8 26.5 - - + +
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Residues in contact with VAL 121 (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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50D ALA* 3.6 31.0 - - + +
53D LEU* 4.2 9.9 - - + -
54D THR* 3.6 29.2 - - - +
57D ILE* 4.4 22.9 - - + -
120F LEU* 1.3 73.6 - - - +
122F SER* 1.3 69.8 + - - +
127F GLN* 3.8 1.2 - - - -
128F ALA* 2.8 27.2 + - + -
129F ALA* 2.8 28.1 + - + +
131F VAL* 4.2 13.2 - - + -
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Residues in contact with SER 122 (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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54D THR* 3.8 23.7 + - - +
57D ILE* 5.9 0.2 - - - +
120F LEU* 4.0 10.2 + - - +
121F VAL* 1.3 79.1 + - - +
123F ARG* 1.3 61.5 + - - +
124F GLY 3.7 14.4 + - - -
125F TRP 5.3 0.2 - - - -
126F GLU 3.1 16.6 + - - -
127F GLN* 4.0 14.9 + - - +
128F ALA 4.2 0.4 - - - +
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Residues in contact with ARG 123 (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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57D ILE* 3.8 30.6 + - + +
58D ASP* 3.0 31.5 + - - -
83D ASP* 5.5 4.6 + - - -
85D LYS* 4.9 17.4 - - - +
122F SER* 1.3 75.2 - - - +
124F GLY* 1.3 59.4 + - - +
125F TRP* 3.4 0.7 + - - -
126F GLU* 2.6 41.1 + - + +
128F ALA* 3.4 34.2 + - + +
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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