Contacts of the strand formed by residues 152 - 156 (chain I) in PDB entry 3J7Y
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 MET 152 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2194A U 5.5 0.4 - - - -
97I ALA 4.0 0.2 - - - +
99I CYS* 2.8 40.1 + - + +
101I ASN* 3.3 55.0 - - + +
109I LYS* 3.8 27.1 - - + +
123I MET* 3.6 31.9 - - + +
124I LYS 3.5 15.9 - - - +
125I VAL* 3.5 27.6 - - + -
151I ASN* 1.3 79.3 + - - +
153I LEU* 1.3 69.7 + - - +
154I LEU* 4.1 4.6 - - + +
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Residues in contact with LEU 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ILE* 5.3 6.1 - - + -
90I PHE* 5.9 1.1 - - + -
96I ILE* 3.8 28.9 - - + -
97I ALA 3.4 2.0 - - - -
98I VAL* 3.9 11.0 - - + -
122I LEU 4.4 0.7 - - - -
124I LYS* 2.8 37.8 + - - +
126I PHE* 3.6 32.1 - - + -
131I LEU* 3.9 24.7 - - + -
147I PHE* 3.5 35.7 - - + -
151I ASN* 3.4 1.9 + - - +
152I MET* 1.3 75.3 - - - +
154I LEU* 1.3 62.8 + - - +
155I VAL* 4.6 11.4 - - + -
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Residues in contact with LEU 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I MET 3.8 0.3 - - - +
96I ILE* 3.7 1.0 - - - -
97I ALA* 2.5 60.3 + - + +
99I CYS* 3.7 18.8 - - + -
116I LEU* 4.9 2.0 - - + -
121I ILE* 3.6 20.6 - - + +
122I LEU 3.2 7.4 - - - -
123I MET* 3.4 23.8 - - + -
152I MET* 4.1 10.1 - - + +
153I LEU* 1.3 82.7 - - - +
155I VAL* 1.3 61.1 + - - +
156I SER 3.8 1.3 + - - -
161I VAL* 4.5 10.1 - - + -
164I MET* 3.5 40.6 - - + -
176I LEU* 5.0 1.6 - - + -
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Residues in contact with VAL 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I VAL* 3.6 26.0 - - + -
90I PHE* 5.5 1.3 - - + +
93I ASN* 3.2 27.1 - - + +
95I MET 4.0 1.8 - - - -
96I ILE* 4.3 18.2 - - + -
120I LYS 5.1 0.2 - - - +
121I ILE* 3.9 0.9 - - - +
122I LEU* 2.8 55.4 + - + +
124I LYS* 5.0 9.2 - - + -
126I PHE* 5.5 3.8 - - + -
153I LEU* 4.6 13.0 - - + -
154I LEU* 1.3 72.6 - - - +
156I SER* 1.3 58.2 + - - +
157I GLU 4.3 0.5 + - - -
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Residues in contact with SER 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ASN* 3.6 6.7 - - - +
94I ARG* 2.8 26.9 + - - +
95I MET* 2.8 36.7 + - - +
121I ILE* 3.6 27.5 - - - +
155I VAL* 1.3 73.3 - - - +
157I GLU* 1.3 54.2 + - - +
158I GLU 2.8 31.8 + - - +
159I PRO* 3.3 9.6 - - - +
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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