Contacts of the strand formed by residues 71 - 78 (chain A) in PDB entry 4CEC
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 LYS 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A HIS* 3.3 9.7 - - - +
68A LEU 2.9 32.2 + - - +
69A GLU* 3.4 23.4 + - - +
70A GLY* 1.3 81.9 - - - +
72A VAL* 1.3 65.5 + - - +
88A VAL* 3.8 29.2 - - + -
89A ILE 4.0 6.5 - - - +
90A PRO* 4.4 10.3 - - + -
172A LEU* 4.1 9.9 - - + -
1211A SO4 2.9 39.4 + - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A CYS* 3.3 29.4 - - - -
66A THR 3.6 2.9 - - - -
67A HIS* 3.7 25.8 - - + +
71A LYS* 1.3 75.4 - - - +
73A ILE* 1.3 67.6 + - - +
74A LEU* 4.3 0.9 - - + +
88A VAL* 3.4 5.9 - - - +
89A ILE* 2.9 60.2 + - + +
90A PRO 4.1 2.5 - - - +
91A ALA* 3.8 22.4 - - - -
92A GLU* 3.9 7.0 - - + +
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Residues in contact with ILE 73 (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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64A ASP 3.8 1.2 - - - +
65A CYS* 3.5 2.4 - - - -
66A THR* 2.7 52.6 + - + +
68A LEU* 4.0 26.2 - - + +
72A VAL* 1.3 77.3 - - - +
74A LEU* 1.3 62.0 + - - +
75A VAL* 3.9 20.5 + - + +
86A ALA* 4.3 2.9 - - + -
87A GLU 3.4 9.9 - - - +
88A VAL* 4.3 6.5 - - + -
158A LEU* 5.8 2.7 - - + -
159A LYS* 5.6 2.0 - - + -
162A ILE* 3.8 28.7 - - + -
172A LEU* 4.8 6.3 - - + -
176A VAL* 3.9 31.0 - - + -
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Residues in contact with LEU 74 (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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63A LEU* 4.4 14.4 - - + -
64A ASP 3.7 17.3 - - - +
65A CYS* 4.4 2.9 - - + +
72A VAL* 3.9 2.7 - - + -
73A ILE* 1.3 71.7 - - - +
75A VAL* 1.3 59.3 + - - +
86A ALA* 3.1 4.7 - - - +
87A GLU* 2.9 49.7 + - + +
89A ILE* 4.1 19.7 - - + -
92A GLU* 3.5 23.8 - - + +
96A GLU 4.4 0.2 - - - +
97A THR* 4.0 22.7 - - + +
100A PHE* 3.7 41.0 - - + -
116A ASP* 4.4 3.6 - - - +
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Residues in contact with VAL 75 (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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62A GLN 3.8 0.2 - - - +
63A LEU* 3.4 6.9 - - - +
64A ASP* 2.7 55.1 + - - +
66A THR* 4.9 4.7 - - + -
73A ILE* 3.9 23.3 - - + +
74A LEU* 1.3 77.7 - - - +
76A ALA* 1.3 70.5 + - - +
77A VAL* 4.1 13.7 - - + -
84A ILE* 4.1 16.8 - - + -
85A GLU 3.4 10.5 - - - +
86A ALA* 4.0 6.3 - - + -
100A PHE* 4.0 4.0 - - - -
154A MET* 4.1 8.3 - - + -
158A LEU* 4.2 13.2 - - + -
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Residues in contact with ALA 76 (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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61A TRP* 3.8 9.3 - - + -
62A GLN 3.4 6.3 - - - +
63A LEU* 4.1 7.9 - - + -
75A VAL* 1.3 74.0 - - - +
77A VAL* 1.3 62.1 + - - +
84A ILE* 3.3 6.1 - - - +
85A GLU 2.9 32.4 + - - +
100A PHE* 3.7 18.0 - - + -
104A LEU* 3.7 33.7 - - + -
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Residues in contact with VAL 77 (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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61A TRP* 3.2 6.7 - - - -
62A GLN* 2.8 54.9 + - + +
64A ASP* 4.7 5.2 - - + -
75A VAL* 4.1 5.8 - - + -
76A ALA* 1.3 75.9 - - - +
78A HIS* 1.3 71.0 + - - +
79A VAL* 3.3 8.1 + - + +
82A GLY* 4.1 11.9 - - - -
83A TYR 3.5 8.5 - - - +
84A ILE* 4.0 9.2 - - + -
150A VAL* 6.3 3.1 - - + -
151A ILE* 5.4 3.6 - - + -
154A MET* 3.4 39.0 - - + -
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Residues in contact with HIS 78 (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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57A SER 3.9 1.4 + - - -
58A PRO 2.7 31.2 + - - -
60A ILE 3.9 8.7 - - - -
61A TRP* 3.4 33.2 - + + -
77A VAL* 1.3 68.8 - - - +
79A VAL* 1.3 58.6 + - - +
80A ALA* 4.1 22.2 - - + -
81A SER* 2.7 31.9 + - - +
82A GLY* 2.8 33.1 + - - -
83A TYR 2.9 14.4 + - - +
200A ILE* 3.5 32.6 - - + +
203A ILE* 4.3 14.8 - - + -
204A ILE* 4.7 2.1 - - + +
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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