Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 1PJP
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 GLN 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.6 24.5 + - + +
19A GLY* 3.7 14.8 + - - +
20A THR* 3.5 6.6 - - - +
21A GLU* 3.5 28.7 - - - +
22A CYS* 3.9 0.9 - - - -
139A ALA* 3.0 5.7 - - - +
140A GLY 2.8 34.7 + - - +
144A THR* 4.3 15.5 - - + +
152A SER* 3.4 27.4 + - - +
154A THR* 3.2 23.7 + - - +
155A LEU* 1.3 73.5 - - - +
157A GLU* 1.3 60.3 + - - +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.3 1.3 - - - -
19A GLY* 3.4 1.3 - - - -
20A THR* 2.8 42.4 + - - +
22A CYS* 3.2 22.9 - - - +
27A ARG* 3.0 42.1 + - - -
137A ARG* 2.9 40.6 + - + +
138A VAL 3.3 13.5 - - - +
139A ALA* 4.3 3.4 - - + -
156A GLN* 1.3 72.8 - - - +
158A VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.7 23.1 - - + +
17A ILE 4.2 0.2 - - - +
18A GLY 3.7 13.9 - - - +
19A GLY* 3.8 1.6 - - - -
137A ARG* 3.1 7.9 - - - +
138A VAL* 2.9 45.0 + - + -
157A GLU* 1.3 76.3 - - - +
159A LYS* 1.3 63.0 + - - +
160A LEU* 3.7 23.5 + - + -
188A LYS* 3.6 39.3 - - + -
189A SER 4.4 7.2 - - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 3.8 38.3 - - + +
136A CYS 3.2 18.8 - - - +
137A ARG* 3.6 33.4 - - - +
158A VAL* 1.3 76.0 - - - +
160A LEU* 1.3 61.9 + - - +
188A LYS* 2.9 36.0 + - - +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 3.4 6.4 - - - -
136A CYS* 2.8 36.3 + - - +
138A VAL* 3.6 27.6 - - + +
158A VAL* 3.7 17.0 + - + -
159A LYS* 1.3 82.5 - - - +
161A ARG* 1.3 61.9 + - - +
162A LEU 3.9 0.5 + - - -
183A VAL* 3.5 31.8 - - + +
184A GLY* 4.4 8.1 - - - +
185A ASN 5.8 0.2 - - - +
188A LYS* 3.7 37.5 - - + +
189A SER* 3.9 1.6 - - - +
190A ALA 4.2 14.1 - - - +
199A LEU* 5.1 1.1 - - + -
226A ALA* 6.3 0.7 - - + -
228A PHE* 4.5 7.2 - - + -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO* 4.7 1.4 - - - +
133A GLY* 3.4 32.5 + - - +
134A ARG 3.6 3.1 - - - -
135A MET* 3.4 22.3 - - + +
160A LEU* 1.3 72.8 - - - +
162A LEU* 1.3 77.6 + - - +
163A MET* 3.1 43.2 - - + +
164A ASP* 4.5 10.3 + - - -
183A VAL* 3.7 2.4 - - - -
184A GLY* 2.9 28.0 + - - +
185A ASN* 4.5 20.5 - - + +
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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