Contacts of the strand formed by residues 90 - 95 (chain A) in PDB entry 5EN1
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY* 4.4 2.3 - - - +
83A PRO* 4.2 24.2 - - + -
84A HIS 3.2 11.0 - - - +
85A SER* 3.7 14.8 - - - +
89A ARG* 1.3 80.4 - - - +
91A VAL* 1.3 70.2 + - - +
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Residues in contact with VAL 91 (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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25A ILE* 3.9 11.2 - - + -
26A GLY 3.6 9.2 - - - +
27A GLY* 3.5 21.3 - - - +
28A LEU* 3.8 23.6 - - + -
29A SER 5.0 0.2 - - - +
41A TYR* 4.2 3.1 - - - +
83A PRO* 5.8 0.3 - - - +
84A HIS* 2.7 43.4 + - + +
86A ILE* 3.7 30.7 - - + +
89A ARG 3.9 9.6 - - - +
90A VAL* 1.3 82.5 - - - +
92A GLU* 1.3 61.5 + - - +
93A PRO* 3.1 11.4 - - + +
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Residues in contact with GLU 92 (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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24A PHE* 3.7 4.0 - - - +
25A ILE* 4.6 0.9 - - - -
26A GLY* 2.9 39.7 + - - +
27A GLY* 5.3 0.9 - - - -
91A VAL* 1.3 72.9 - - - +
93A PRO* 1.4 64.6 - - + +
94A LYS* 3.3 39.1 + - + +
110A THR* 5.1 5.9 - - - +
163A HIS* 5.8 4.8 + - - +
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Residues in contact with PRO 93 (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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23A LEU* 4.4 4.3 - - + -
24A PHE 3.3 6.7 - - - +
25A ILE* 4.1 11.6 - - + -
41A TYR* 3.5 19.3 - - - +
79A MET* 3.4 23.1 - - - +
82A ARG* 3.8 25.1 + - + -
84A HIS* 3.6 24.2 - - + +
91A VAL 3.1 14.1 - - - +
92A GLU* 1.4 85.5 - - + +
94A LYS* 1.3 64.8 + - - +
163A HIS* 4.0 6.6 + - - -
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Residues in contact with LYS 94 (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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23A LEU* 3.6 7.8 - - - +
24A PHE* 2.7 43.4 + - + +
79A MET* 4.4 4.3 - - - -
92A GLU* 3.3 42.0 + - + +
93A PRO* 1.3 79.7 - - - +
95A ARG* 1.3 66.8 + - - +
108A HIS 4.1 11.9 + - - -
110A THR* 2.7 34.6 + - - +
163A HIS* 4.0 16.2 - - + +
167A ASP* 5.0 2.7 - - - +
1B A 3.3 29.3 + - - +
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Residues in contact with ARG 95 (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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19A GLN 5.9 0.9 - - - +
20A PHE 4.8 1.4 + - - -
22A LYS 4.0 6.7 - - - +
23A LEU* 4.5 2.9 - - + -
72A MET* 4.1 17.6 - - - +
75A VAL* 3.6 30.2 - - + +
76A ASP* 2.7 38.4 + - - +
79A MET* 4.4 3.9 - - + +
94A LYS* 1.3 77.7 - - - +
96A ALA* 1.3 65.9 + - - +
97A VAL* 4.5 3.6 - - - +
164A ASP* 2.8 40.7 + - - +
167A ASP* 4.1 18.7 + - + +
168A LYS* 3.8 42.2 - - - +
171A LEU* 4.6 20.9 - - + +
1B A 3.7 8.3 + - - +
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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