Contacts of the strand formed by residues 153 - 158 (chain C) in PDB entry 3PRJ
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 ASN 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C GLY 2.8 13.8 + - - +
123C TYR* 3.3 34.1 - - + -
124C LYS 3.1 24.4 + - - +
151C ASN 3.5 3.6 + - - +
152C LEU* 1.3 75.5 - - - +
154C LEU* 1.3 59.0 + - - +
155C GLN* 3.2 19.1 + - - +
187C GLU* 3.0 26.7 + - - +
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Residues in contact with LEU 154 (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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116C ILE* 4.3 11.9 - - + -
117C VAL* 4.1 10.3 - - + -
120C SER* 4.6 3.8 - - - -
124C LYS* 3.5 27.1 - - + -
126C VAL* 4.0 15.9 - - + -
144C PHE* 3.6 47.2 - - + +
152C LEU* 3.8 39.4 - - + +
153C ASN* 1.3 75.0 + - - +
155C GLN* 1.3 68.5 + - - +
156C VAL* 3.9 7.6 + - - +
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Residues in contact with GLN 155 (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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123C TYR* 3.7 28.7 - - + +
124C LYS 2.9 11.4 + - - +
125C ILE* 3.5 5.4 - - + +
126C VAL* 2.7 35.3 + - - +
153C ASN* 3.2 29.1 + - - +
154C LEU* 1.3 79.9 + - - +
156C VAL* 1.3 59.8 + - - +
157C LEU* 3.9 0.6 + - + -
183C ASP* 5.7 4.0 - - - -
185C THR* 5.2 0.7 + - - -
187C GLU* 3.8 34.7 - - - +
188C GLY* 3.9 5.9 + - - -
191C ALA* 4.0 21.8 - - + -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C VAL* 3.4 7.2 - - + +
137C ALA* 4.0 30.7 - - + +
140C ILE* 4.1 17.0 - - + -
141C ARG* 3.8 35.2 - - + +
144C PHE* 3.9 26.9 - - + -
154C LEU 4.4 4.0 - - - +
155C GLN* 1.3 75.9 + - - +
157C LEU* 1.3 76.5 + - - +
183C ASP* 3.7 18.4 + - - +
213C THR* 4.1 6.0 - - + +
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Residues in contact with LEU 157 (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 ILE* 3.8 20.0 - - + -
126C VAL 2.8 9.8 + - - +
127C THR* 3.3 18.5 - - + +
128C GLU* 2.8 33.3 + - - +
137C ALA* 5.5 1.7 - - - +
156C VAL* 1.3 88.2 - - - +
158C SER* 1.3 57.8 + - - +
180C ILE* 4.2 2.9 - - + -
181C GLY 3.3 13.9 - - - +
182C GLY* 3.7 12.6 - - - -
183C ASP 5.1 0.7 - - - +
188C GLY* 4.6 1.8 - - - +
191C ALA* 3.8 26.0 - - + +
192C VAL* 3.8 20.6 - - + +
195C LEU* 3.6 28.9 - - + -
213C THR* 4.7 2.0 - - - -
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Residues in contact with SER 158 (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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128C GLU* 3.8 10.0 + - - +
133C PRO* 5.1 0.7 - - - +
137C ALA* 4.7 2.7 - - - -
157C LEU* 1.3 72.5 - - - +
159C ASN* 1.3 65.9 + - - +
160C PRO* 3.7 8.8 - - - +
179C LEU 3.8 0.3 - - - +
180C ILE* 3.4 3.6 - - - +
181C GLY 2.8 38.3 + - - +
213C THR* 4.1 20.6 - - - +
216C SER* 3.4 18.8 + - - -
217C GLU* 3.5 24.6 + - - +
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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