Contacts of the strand formed by residues 116 - 122 (chain C) in PDB entry 3PRO
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 VAL 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASN* 3.0 28.1 + - - +
113C LEU* 3.1 24.0 + - + +
115C GLY* 1.3 79.0 + - - +
117C GLN* 1.3 62.1 + - - +
119C TRP* 3.6 34.5 - - + -
130C VAL* 4.1 6.7 - - + -
131C LYS 3.8 10.1 - - - +
132C VAL* 4.1 1.6 - - + -
133C ASP* 5.4 0.2 - - - -
139C ALA* 4.1 29.8 - - + +
140C GLY* 4.3 5.8 - - - +
143C PHE* 4.0 22.0 - - + -
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Residues in contact with GLN 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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122A ASN* 2.9 28.5 + - - +
162A ASN* 3.8 12.9 - - - +
178A SER* 4.6 5.7 + - - -
115C GLY 3.6 0.4 + - - -
116C VAL* 1.3 73.6 - - - +
118C SER* 1.3 59.6 + - - +
131C LYS* 2.7 21.5 + - + +
132C VAL 4.5 0.2 - - - -
133C ASP* 3.0 33.7 + - - +
159C SER* 2.7 41.2 + - - -
160C PRO 3.4 6.5 + - - -
161C GLY 3.1 20.6 + - - -
162C LYS* 4.1 0.4 - - - +
163C LEU* 3.1 34.4 - - + +
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 3.9 16.5 - - - +
120A THR 3.1 18.4 - - - -
121A ALA* 4.1 3.4 - - - -
133A GLN* 4.9 0.2 + - - -
178A SER* 4.5 7.1 + - - -
180A LEU* 5.3 1.8 - - - -
116C VAL* 3.8 1.0 - - - +
117C GLN* 1.3 82.1 - - - +
119C TRP* 1.3 73.5 + - - +
120C TYR* 4.3 4.4 - - - -
130C VAL* 3.4 2.1 - - - +
131C LYS* 2.7 48.6 + - - +
163C LEU* 4.5 5.6 - - - +
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Residues in contact with TRP 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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119A VAL* 3.7 0.3 - - - -
120A THR* 3.0 53.0 + - + -
122A ASN* 4.0 22.9 - - + -
127A ALA* 5.1 4.3 - - + -
95C MET* 3.5 20.0 - - + +
98C LEU* 3.7 22.4 - - + -
99C ASP* 2.9 27.2 + - - +
102C ALA* 3.6 32.5 - - + -
113C LEU* 3.8 9.0 - - + -
116C VAL* 3.6 22.2 - - + -
118C SER* 1.3 93.7 - - - +
120C TYR* 1.3 67.5 + - - +
129C VAL 2.9 13.7 - - - +
130C VAL* 4.0 13.7 - - + -
143C PHE* 3.6 19.5 - + - -
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Residues in contact with TYR 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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115A THR 5.1 0.4 - - - -
116A ALA* 3.4 22.2 - - + -
117A LYS 4.2 4.7 - - - +
118A ASN 4.2 0.4 - - - +
119A VAL* 3.6 35.4 - - + -
133A GLN* 3.1 33.6 + - - -
95C MET* 3.7 10.4 - - - -
118C SER* 4.3 9.2 - - - -
119C TRP* 1.3 83.8 - - - +
121C VAL* 1.3 71.9 + - - +
122C ASP* 3.9 14.5 - - + -
128C VAL* 4.0 5.6 - - - +
129C VAL* 2.7 65.6 + - + +
131C LYS* 3.3 20.3 - - + -
155C ARG* 5.4 1.0 + - - -
157C GLU* 5.1 1.7 + - - -
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Residues in contact with VAL 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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116A ALA* 4.8 2.9 - - - +
117A LYS 4.4 11.5 + - - +
118A ASN* 5.1 1.0 + - + -
88C LEU* 3.9 27.4 - - + -
91C LEU* 3.7 34.3 - - + +
92C GLN* 3.7 17.7 - - + +
95C MET* 3.7 31.1 - - + -
120C TYR* 1.3 82.5 - - - +
122C ASP* 1.3 60.4 + - - +
123C PRO* 3.5 13.6 - - + +
127C ALA 4.0 3.8 - - - -
128C VAL* 4.2 4.7 - - + +
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Residues in contact with ASP 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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115A THR 4.1 15.4 - - - +
116A ALA* 5.1 0.3 - - - +
91C LEU* 5.0 0.2 - - - -
120C TYR* 3.4 11.1 + - + -
121C VAL* 1.3 73.6 - - - +
123C PRO* 1.3 70.6 - - - +
124C ARG* 4.1 12.2 + - - +
125C SER* 2.6 40.0 + - - +
126C ASN 3.1 8.0 + - - -
127C ALA 2.8 19.4 + - - +
129C VAL* 3.5 20.2 - - + -
155C ARG* 3.3 12.2 + - - -
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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